biointerchange 0.2.2 → 1.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (55) hide show
  1. data/Gemfile +1 -0
  2. data/README.md +269 -19
  3. data/VERSION +1 -1
  4. data/examples/bininda_emonds_mammals.new +1 -0
  5. data/examples/rdfization.rb +17 -0
  6. data/examples/tree1.new +1 -0
  7. data/examples/tree2.new +1 -0
  8. data/examples/vocabulary.rb +26 -5
  9. data/generators/javaify.rb +12 -18
  10. data/generators/make_supplement_releases.rb +2 -0
  11. data/generators/pythonify.rb +21 -8
  12. data/generators/rdfxml.rb +15 -1
  13. data/lib/biointerchange/cdao.rb +2014 -0
  14. data/lib/biointerchange/core.rb +70 -77
  15. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
  16. data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
  17. data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
  18. data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
  19. data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
  20. data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
  21. data/lib/biointerchange/registry.rb +50 -8
  22. data/lib/biointerchange/so.rb +150 -0
  23. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
  24. data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
  25. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
  26. data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
  27. data/spec/phylogenetics_spec.rb +79 -0
  28. data/supplemental/java/biointerchange/pom.xml +1 -1
  29. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
  30. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
  31. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
  32. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
  33. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
  34. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
  35. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
  36. data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
  37. data/supplemental/python/biointerchange/cdao.py +2021 -0
  38. data/supplemental/python/biointerchange/faldo.py +37 -38
  39. data/supplemental/python/biointerchange/gff3o.py +156 -157
  40. data/supplemental/python/biointerchange/goxref.py +172 -172
  41. data/supplemental/python/biointerchange/gvf1o.py +428 -429
  42. data/supplemental/python/biointerchange/sio.py +3133 -3134
  43. data/supplemental/python/biointerchange/so.py +6626 -6527
  44. data/supplemental/python/biointerchange/sofa.py +790 -791
  45. data/supplemental/python/example.py +23 -5
  46. data/supplemental/python/setup.py +2 -2
  47. data/web/about.html +1 -0
  48. data/web/api.html +223 -15
  49. data/web/biointerchange.js +27 -6
  50. data/web/cli.html +8 -3
  51. data/web/index.html +6 -2
  52. data/web/ontologies.html +3 -0
  53. data/web/service/rdfizer.fcgi +7 -15
  54. data/web/webservices.html +6 -2
  55. metadata +30 -3
@@ -9,1032 +9,1032 @@ class GOXRef:
9
9
  def AGI_LocusCode(cls):
10
10
  """Returns the link-out URI for objects of "Arabidopsis Genome Initiative".
11
11
  """
12
- RDF::URI.new("http://arabidopsis.org/servlets/TairObject?type=locus&name=")
12
+ cls.Namespace("http://arabidopsis.org/servlets/TairObject?type=locus&name=")
13
13
 
14
14
  @classmethod
15
15
  def ApiDB_PlasmoDB(cls):
16
16
  """Returns the link-out URI for objects of "PlasmoDB Plasmodium Genome Resource".
17
17
  """
18
- RDF::URI.new("http://www.plasmodb.org/gene/")
18
+ cls.Namespace("http://www.plasmodb.org/gene/")
19
19
 
20
20
  @classmethod
21
21
  def AraCyc(cls):
22
22
  """Returns the link-out URI for objects of "AraCyc metabolic pathway database for Arabidopsis thaliana".
23
23
  """
24
- RDF::URI.new("http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=")
24
+ cls.Namespace("http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=")
25
25
 
26
26
  @classmethod
27
27
  def ASAP(cls):
28
28
  """Returns the link-out URI for objects of "A Systematic Annotation Package for Community Analysis of Genomes".
29
29
  """
30
- RDF::URI.new("https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=")
30
+ cls.Namespace("https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=")
31
31
 
32
32
  @classmethod
33
33
  def AspGD(cls):
34
34
  """Returns the link-out URI for objects of "Aspergillus Genome Database".
35
35
  """
36
- RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=")
36
+ cls.Namespace("http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=")
37
37
 
38
38
  @classmethod
39
39
  def AspGD_LOCUS(cls):
40
40
  """Returns the link-out URI for objects of "Aspergillus Genome Database".
41
41
  """
42
- RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=")
42
+ cls.Namespace("http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=")
43
43
 
44
44
  @classmethod
45
45
  def AspGD_REF(cls):
46
46
  """Returns the link-out URI for objects of "Aspergillus Genome Database".
47
47
  """
48
- RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=")
48
+ cls.Namespace("http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=")
49
49
 
50
50
  @classmethod
51
51
  def BFO(cls):
52
52
  """Returns the link-out URI for objects of "Basic Formal Ontology".
53
53
  """
54
- RDF::URI.new("http://purl.obolibrary.org/obo/BFO_")
54
+ cls.Namespace("http://purl.obolibrary.org/obo/BFO_")
55
55
 
56
56
  @classmethod
57
57
  def BioCyc(cls):
58
58
  """Returns the link-out URI for objects of "BioCyc collection of metabolic pathway databases".
59
59
  """
60
- RDF::URI.new("http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=")
60
+ cls.Namespace("http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=")
61
61
 
62
62
  @classmethod
63
63
  def BIOMD(cls):
64
64
  """Returns the link-out URI for objects of "BioModels Database".
65
65
  """
66
- RDF::URI.new("http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=")
66
+ cls.Namespace("http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=")
67
67
 
68
68
  @classmethod
69
69
  def BRENDA(cls):
70
70
  """Returns the link-out URI for objects of "BRENDA, The Comprehensive Enzyme Information System".
71
71
  """
72
- RDF::URI.new("http://www.brenda-enzymes.info/php/result_flat.php4?ecno=")
72
+ cls.Namespace("http://www.brenda-enzymes.info/php/result_flat.php4?ecno=")
73
73
 
74
74
  @classmethod
75
75
  def Broad_MGG(cls):
76
76
  """Returns the link-out URI for objects of "Magnaporthe grisea Database".
77
77
  """
78
- RDF::URI.new("http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S")
78
+ cls.Namespace("http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S")
79
79
 
80
80
  @classmethod
81
81
  def CASGEN(cls):
82
82
  """Returns the link-out URI for objects of "Catalog of Fishes genus database".
83
83
  """
84
- RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=")
84
+ cls.Namespace("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=")
85
85
 
86
86
  @classmethod
87
87
  def CASREF(cls):
88
88
  """Returns the link-out URI for objects of "Catalog of Fishes publications database".
89
89
  """
90
- RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=")
90
+ cls.Namespace("http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=")
91
91
 
92
92
  @classmethod
93
93
  def CASSPC(cls):
94
94
  """Returns the link-out URI for objects of "Catalog of Fishes species database".
95
95
  """
96
- RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979")
96
+ cls.Namespace("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979")
97
97
 
98
98
  @classmethod
99
99
  def CDD(cls):
100
100
  """Returns the link-out URI for objects of "Conserved Domain Database at NCBI".
101
101
  """
102
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=")
102
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=")
103
103
 
104
104
  @classmethod
105
105
  def CGD(cls):
106
106
  """Returns the link-out URI for objects of "Candida Genome Database".
107
107
  """
108
- RDF::URI.new("http://www.candidagenome.org/cgi-bin/locus.pl?dbid=")
108
+ cls.Namespace("http://www.candidagenome.org/cgi-bin/locus.pl?dbid=")
109
109
 
110
110
  @classmethod
111
111
  def CGD_LOCUS(cls):
112
112
  """Returns the link-out URI for objects of "Candida Genome Database".
113
113
  """
114
- RDF::URI.new("http://www.candidagenome.org/cgi-bin/locus.pl?locus=")
114
+ cls.Namespace("http://www.candidagenome.org/cgi-bin/locus.pl?locus=")
115
115
 
116
116
  @classmethod
117
117
  def CGD_REF(cls):
118
118
  """Returns the link-out URI for objects of "Candida Genome Database".
119
119
  """
120
- RDF::URI.new("http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=")
120
+ cls.Namespace("http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=")
121
121
 
122
122
  @classmethod
123
123
  def CHEBI(cls):
124
124
  """Returns the link-out URI for objects of "Chemical Entities of Biological Interest".
125
125
  """
126
- RDF::URI.new("http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:")
126
+ cls.Namespace("http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:")
127
127
 
128
128
  @classmethod
129
129
  def CL(cls):
130
130
  """Returns the link-out URI for objects of "Cell Type Ontology".
131
131
  """
132
- RDF::URI.new("http://purl.obolibrary.org/obo/CL_")
132
+ cls.Namespace("http://purl.obolibrary.org/obo/CL_")
133
133
 
134
134
  @classmethod
135
135
  def COG_Cluster(cls):
136
136
  """Returns the link-out URI for objects of "NCBI COG cluster".
137
137
  """
138
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=")
138
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=")
139
139
 
140
140
  @classmethod
141
141
  def COG_Function(cls):
142
142
  """Returns the link-out URI for objects of "NCBI COG function".
143
143
  """
144
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=")
144
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=")
145
145
 
146
146
  @classmethod
147
147
  def COG_Pathway(cls):
148
148
  """Returns the link-out URI for objects of "NCBI COG pathway".
149
149
  """
150
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=")
150
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=")
151
151
 
152
152
  @classmethod
153
153
  def CORUM(cls):
154
154
  """Returns the link-out URI for objects of "CORUM - the Comprehensive Resource of Mammalian protein complexes".
155
155
  """
156
- RDF::URI.new("http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=")
156
+ cls.Namespace("http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=")
157
157
 
158
158
  @classmethod
159
159
  def dbSNP(cls):
160
160
  """Returns the link-out URI for objects of "NCBI dbSNP".
161
161
  """
162
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=")
162
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=")
163
163
 
164
164
  @classmethod
165
165
  def DDBJ(cls):
166
166
  """Returns the link-out URI for objects of "DNA Databank of Japan".
167
167
  """
168
- RDF::URI.new("http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=")
168
+ cls.Namespace("http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=")
169
169
 
170
170
  @classmethod
171
171
  def dictyBase(cls):
172
172
  """Returns the link-out URI for objects of "dictyBase".
173
173
  """
174
- RDF::URI.new("http://dictybase.org/gene/")
174
+ cls.Namespace("http://dictybase.org/gene/")
175
175
 
176
176
  @classmethod
177
177
  def dictyBase_gene_name(cls):
178
178
  """Returns the link-out URI for objects of "dictyBase".
179
179
  """
180
- RDF::URI.new("http://dictybase.org/gene/")
180
+ cls.Namespace("http://dictybase.org/gene/")
181
181
 
182
182
  @classmethod
183
183
  def dictyBase_REF(cls):
184
184
  """Returns the link-out URI for objects of "dictyBase literature references".
185
185
  """
186
- RDF::URI.new("http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=")
186
+ cls.Namespace("http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=")
187
187
 
188
188
  @classmethod
189
189
  def DOI(cls):
190
190
  """Returns the link-out URI for objects of "Digital Object Identifier".
191
191
  """
192
- RDF::URI.new("http://dx.doi.org/DOI:")
192
+ cls.Namespace("http://dx.doi.org/DOI:")
193
193
 
194
194
  @classmethod
195
195
  def EC(cls):
196
196
  """Returns the link-out URI for objects of "Enzyme Commission".
197
197
  """
198
- RDF::URI.new("http://www.expasy.org/enzyme/")
198
+ cls.Namespace("http://www.expasy.org/enzyme/")
199
199
 
200
200
  @classmethod
201
201
  def EchoBASE(cls):
202
202
  """Returns the link-out URI for objects of "EchoBASE post-genomic database for Escherichia coli".
203
203
  """
204
- RDF::URI.new("http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=")
204
+ cls.Namespace("http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=")
205
205
 
206
206
  @classmethod
207
207
  def ECK(cls):
208
208
  """Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
209
209
  """
210
- RDF::URI.new("http://www.ecogene.org/geneInfo.php?eck_id=")
210
+ cls.Namespace("http://www.ecogene.org/geneInfo.php?eck_id=")
211
211
 
212
212
  @classmethod
213
213
  def EcoCyc(cls):
214
214
  """Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
215
215
  """
216
- RDF::URI.new("http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=")
216
+ cls.Namespace("http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=")
217
217
 
218
218
  @classmethod
219
219
  def EcoCyc_REF(cls):
220
220
  """Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
221
221
  """
222
- RDF::URI.new("http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=")
222
+ cls.Namespace("http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=")
223
223
 
224
224
  @classmethod
225
225
  def ECOGENE(cls):
226
226
  """Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
227
227
  """
228
- RDF::URI.new("http://www.ecogene.org/geneInfo.php?eg_id=")
228
+ cls.Namespace("http://www.ecogene.org/geneInfo.php?eg_id=")
229
229
 
230
230
  @classmethod
231
231
  def EMBL(cls):
232
232
  """Returns the link-out URI for objects of "EMBL Nucleotide Sequence Database".
233
233
  """
234
- RDF::URI.new("http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=")
234
+ cls.Namespace("http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=")
235
235
 
236
236
  @classmethod
237
237
  def ENA(cls):
238
238
  """Returns the link-out URI for objects of "European Nucleotide Archive".
239
239
  """
240
- RDF::URI.new("http://www.ebi.ac.uk/ena/data/view/")
240
+ cls.Namespace("http://www.ebi.ac.uk/ena/data/view/")
241
241
 
242
242
  @classmethod
243
243
  def ENSEMBL(cls):
244
244
  """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
245
245
  """
246
- RDF::URI.new("http://www.ensembl.org/id/")
246
+ cls.Namespace("http://www.ensembl.org/id/")
247
247
 
248
248
  @classmethod
249
249
  def ENSEMBL_GeneID(cls):
250
250
  """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
251
251
  """
252
- RDF::URI.new("http://www.ensembl.org/id/")
252
+ cls.Namespace("http://www.ensembl.org/id/")
253
253
 
254
254
  @classmethod
255
255
  def ENSEMBL_ProteinID(cls):
256
256
  """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
257
257
  """
258
- RDF::URI.new("http://www.ensembl.org/id/")
258
+ cls.Namespace("http://www.ensembl.org/id/")
259
259
 
260
260
  @classmethod
261
261
  def ENSEMBL_TranscriptID(cls):
262
262
  """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
263
263
  """
264
- RDF::URI.new("http://www.ensembl.org/id/")
264
+ cls.Namespace("http://www.ensembl.org/id/")
265
265
 
266
266
  @classmethod
267
267
  def ENZYME(cls):
268
268
  """Returns the link-out URI for objects of "Swiss Institute of Bioinformatics enzyme database".
269
269
  """
270
- RDF::URI.new("http://www.expasy.ch/cgi-bin/nicezyme.pl?")
270
+ cls.Namespace("http://www.expasy.ch/cgi-bin/nicezyme.pl?")
271
271
 
272
272
  @classmethod
273
273
  def FBbt(cls):
274
274
  """Returns the link-out URI for objects of "Drosophila gross anatomy".
275
275
  """
276
- RDF::URI.new("http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:")
276
+ cls.Namespace("http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:")
277
277
 
278
278
  @classmethod
279
279
  def GDB(cls):
280
280
  """Returns the link-out URI for objects of "Human Genome Database".
281
281
  """
282
- RDF::URI.new("http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:")
282
+ cls.Namespace("http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:")
283
283
 
284
284
  @classmethod
285
285
  def GenBank(cls):
286
286
  """Returns the link-out URI for objects of "GenBank".
287
287
  """
288
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=")
288
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=")
289
289
 
290
290
  @classmethod
291
291
  def Gene3D(cls):
292
292
  """Returns the link-out URI for objects of "Domain Architecture Classification".
293
293
  """
294
- RDF::URI.new("http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=")
294
+ cls.Namespace("http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=")
295
295
 
296
296
  @classmethod
297
297
  def GeneDB_Gmorsitans(cls):
298
298
  """Returns the link-out URI for objects of "Glossina morsitans GeneDB".
299
299
  """
300
- RDF::URI.new("http://www.genedb.org/genedb/Search?organism=glossina&name=")
300
+ cls.Namespace("http://www.genedb.org/genedb/Search?organism=glossina&name=")
301
301
 
302
302
  @classmethod
303
303
  def GeneDB_Lmajor(cls):
304
304
  """Returns the link-out URI for objects of "Leishmania major GeneDB".
305
305
  """
306
- RDF::URI.new("http://www.genedb.org/genedb/Search?organism=leish&name=")
306
+ cls.Namespace("http://www.genedb.org/genedb/Search?organism=leish&name=")
307
307
 
308
308
  @classmethod
309
309
  def GeneDB_Pfalciparum(cls):
310
310
  """Returns the link-out URI for objects of "Plasmodium falciparum GeneDB".
311
311
  """
312
- RDF::URI.new("http://www.genedb.org/genedb/Search?organism=malaria&name=")
312
+ cls.Namespace("http://www.genedb.org/genedb/Search?organism=malaria&name=")
313
313
 
314
314
  @classmethod
315
315
  def GeneDB_Spombe(cls):
316
316
  """Returns the link-out URI for objects of "Schizosaccharomyces pombe GeneDB".
317
317
  """
318
- RDF::URI.new("http://old.genedb.org/genedb/Search?organism=pombe&name=")
318
+ cls.Namespace("http://old.genedb.org/genedb/Search?organism=pombe&name=")
319
319
 
320
320
  @classmethod
321
321
  def GeneDB_Tbrucei(cls):
322
322
  """Returns the link-out URI for objects of "Trypanosoma brucei GeneDB".
323
323
  """
324
- RDF::URI.new("http://www.genedb.org/genedb/Search?organism=tryp&name=")
324
+ cls.Namespace("http://www.genedb.org/genedb/Search?organism=tryp&name=")
325
325
 
326
326
  @classmethod
327
327
  def GEO(cls):
328
328
  """Returns the link-out URI for objects of "NCBI Gene Expression Omnibus".
329
329
  """
330
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=")
330
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=")
331
331
 
332
332
  @classmethod
333
333
  def GO(cls):
334
334
  """Returns the link-out URI for objects of "Gene Ontology Database".
335
335
  """
336
- RDF::URI.new("http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:")
336
+ cls.Namespace("http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:")
337
337
 
338
338
  @classmethod
339
339
  def GO_REF(cls):
340
340
  """Returns the link-out URI for objects of "Gene Ontology Database references".
341
341
  """
342
- RDF::URI.new("http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:")
342
+ cls.Namespace("http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:")
343
343
 
344
344
  @classmethod
345
345
  def GONUTS(cls):
346
346
  """Returns the link-out URI for objects of "Gene Ontology Normal Usage Tracking System (cls, GONUTS)".
347
347
  """
348
- RDF::URI.new("http://gowiki.tamu.edu/wiki/index.php/")
348
+ cls.Namespace("http://gowiki.tamu.edu/wiki/index.php/")
349
349
 
350
350
  @classmethod
351
351
  def GR(cls):
352
352
  """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
353
353
  """
354
- RDF::URI.new("http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=")
354
+ cls.Namespace("http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=")
355
355
 
356
356
  @classmethod
357
357
  def GR_GENE(cls):
358
358
  """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
359
359
  """
360
- RDF::URI.new("http://www.gramene.org/db/genes/search_gene?acc=")
360
+ cls.Namespace("http://www.gramene.org/db/genes/search_gene?acc=")
361
361
 
362
362
  @classmethod
363
363
  def GR_PROTEIN(cls):
364
364
  """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
365
365
  """
366
- RDF::URI.new("http://www.gramene.org/db/protein/protein_search?acc=")
366
+ cls.Namespace("http://www.gramene.org/db/protein/protein_search?acc=")
367
367
 
368
368
  @classmethod
369
369
  def GR_QTL(cls):
370
370
  """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
371
371
  """
372
- RDF::URI.new("http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=")
372
+ cls.Namespace("http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=")
373
373
 
374
374
  @classmethod
375
375
  def GR_REF(cls):
376
376
  """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
377
377
  """
378
- RDF::URI.new("http://www.gramene.org/db/literature/pub_search?ref_id=")
378
+ cls.Namespace("http://www.gramene.org/db/literature/pub_search?ref_id=")
379
379
 
380
380
  @classmethod
381
381
  def H_invDB_cDNA(cls):
382
382
  """Returns the link-out URI for objects of "H-invitational Database".
383
383
  """
384
- RDF::URI.new("http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=")
384
+ cls.Namespace("http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=")
385
385
 
386
386
  @classmethod
387
387
  def H_invDB_locus(cls):
388
388
  """Returns the link-out URI for objects of "H-invitational Database".
389
389
  """
390
- RDF::URI.new("http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=")
390
+ cls.Namespace("http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=")
391
391
 
392
392
  @classmethod
393
393
  def HAMAP(cls):
394
394
  """Returns the link-out URI for objects of "High-quality Automated and Manual Annotation of microbial Proteomes".
395
395
  """
396
- RDF::URI.new("http://us.expasy.org/unirules/")
396
+ cls.Namespace("http://us.expasy.org/unirules/")
397
397
 
398
398
  @classmethod
399
399
  def HGNC(cls):
400
400
  """Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
401
401
  """
402
- RDF::URI.new("http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:")
402
+ cls.Namespace("http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:")
403
403
 
404
404
  @classmethod
405
405
  def HGNC_gene(cls):
406
406
  """Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
407
407
  """
408
- RDF::URI.new("http://www.genenames.org/data/hgnc_data.php?app_sym=")
408
+ cls.Namespace("http://www.genenames.org/data/hgnc_data.php?app_sym=")
409
409
 
410
410
  @classmethod
411
411
  def HPA(cls):
412
412
  """Returns the link-out URI for objects of "Human Protein Atlas tissue profile information".
413
413
  """
414
- RDF::URI.new("http://www.proteinatlas.org/tissue_profile.php?antibody_id=")
414
+ cls.Namespace("http://www.proteinatlas.org/tissue_profile.php?antibody_id=")
415
415
 
416
416
  @classmethod
417
417
  def HPA_antibody(cls):
418
418
  """Returns the link-out URI for objects of "Human Protein Atlas antibody information".
419
419
  """
420
- RDF::URI.new("http://www.proteinatlas.org/antibody_info.php?antibody_id=")
420
+ cls.Namespace("http://www.proteinatlas.org/antibody_info.php?antibody_id=")
421
421
 
422
422
  @classmethod
423
423
  def IMG(cls):
424
424
  """Returns the link-out URI for objects of "Integrated Microbial Genomes; JGI web site for genome annotation".
425
425
  """
426
- RDF::URI.new("http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=")
426
+ cls.Namespace("http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=")
427
427
 
428
428
  @classmethod
429
429
  def IntAct(cls):
430
430
  """Returns the link-out URI for objects of "IntAct protein interaction database".
431
431
  """
432
- RDF::URI.new("http://www.ebi.ac.uk/intact/search/do/search?searchString=")
432
+ cls.Namespace("http://www.ebi.ac.uk/intact/search/do/search?searchString=")
433
433
 
434
434
  @classmethod
435
435
  def InterPro(cls):
436
436
  """Returns the link-out URI for objects of "InterPro database of protein domains and motifs".
437
437
  """
438
- RDF::URI.new("http://www.ebi.ac.uk/interpro/IEntry?ac=")
438
+ cls.Namespace("http://www.ebi.ac.uk/interpro/IEntry?ac=")
439
439
 
440
440
  @classmethod
441
441
  def ISBN(cls):
442
442
  """Returns the link-out URI for objects of "International Standard Book Number".
443
443
  """
444
- RDF::URI.new("http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=")
444
+ cls.Namespace("http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=")
445
445
 
446
446
  @classmethod
447
447
  def IUPHAR_GPCR(cls):
448
448
  """Returns the link-out URI for objects of "International Union of Pharmacology".
449
449
  """
450
- RDF::URI.new("http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=")
450
+ cls.Namespace("http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=")
451
451
 
452
452
  @classmethod
453
453
  def IUPHAR_RECEPTOR(cls):
454
454
  """Returns the link-out URI for objects of "International Union of Pharmacology".
455
455
  """
456
- RDF::URI.new("http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=")
456
+ cls.Namespace("http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=")
457
457
 
458
458
  @classmethod
459
459
  def JCVI_CMR(cls):
460
460
  """Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
461
461
  """
462
- RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=")
462
+ cls.Namespace("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=")
463
463
 
464
464
  @classmethod
465
465
  def JCVI_EGAD(cls):
466
466
  """Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
467
467
  """
468
- RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=")
468
+ cls.Namespace("http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=")
469
469
 
470
470
  @classmethod
471
471
  def JCVI_GenProp(cls):
472
472
  """Returns the link-out URI for objects of "Genome Properties database at the J. Craig Venter Institute".
473
473
  """
474
- RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=")
474
+ cls.Namespace("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=")
475
475
 
476
476
  @classmethod
477
477
  def JCVI_Medtr(cls):
478
478
  """Returns the link-out URI for objects of "Medicago truncatula genome database at the J. Craig Venter Institute ".
479
479
  """
480
- RDF::URI.new("http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=")
480
+ cls.Namespace("http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=")
481
481
 
482
482
  @classmethod
483
483
  def JCVI_TIGRFAMS(cls):
484
484
  """Returns the link-out URI for objects of "TIGRFAMs HMM collection at the J. Craig Venter Institute".
485
485
  """
486
- RDF::URI.new("http://search.jcvi.org/search?p&q=")
486
+ cls.Namespace("http://search.jcvi.org/search?p&q=")
487
487
 
488
488
  @classmethod
489
489
  def JSTOR(cls):
490
490
  """Returns the link-out URI for objects of "Digital archive of scholarly articles".
491
491
  """
492
- RDF::URI.new("http://www.jstor.org/stable/")
492
+ cls.Namespace("http://www.jstor.org/stable/")
493
493
 
494
494
  @classmethod
495
495
  def KEGG_ENZYME(cls):
496
496
  """Returns the link-out URI for objects of "KEGG Enzyme Database".
497
497
  """
498
- RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?ec:")
498
+ cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?ec:")
499
499
 
500
500
  @classmethod
501
501
  def KEGG_LIGAND(cls):
502
502
  """Returns the link-out URI for objects of "KEGG LIGAND Database".
503
503
  """
504
- RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?cpd:")
504
+ cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?cpd:")
505
505
 
506
506
  @classmethod
507
507
  def KEGG_PATHWAY(cls):
508
508
  """Returns the link-out URI for objects of "KEGG Pathways Database".
509
509
  """
510
- RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?path:")
510
+ cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?path:")
511
511
 
512
512
  @classmethod
513
513
  def KEGG_REACTION(cls):
514
514
  """Returns the link-out URI for objects of "KEGG Reaction Database".
515
515
  """
516
- RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?rn:")
516
+ cls.Namespace("http://www.genome.jp/dbget-bin/www_bget?rn:")
517
517
 
518
518
  @classmethod
519
519
  def LIFEdb(cls):
520
520
  """Returns the link-out URI for objects of "LifeDB".
521
521
  """
522
- RDF::URI.new("http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=")
522
+ cls.Namespace("http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=")
523
523
 
524
524
  @classmethod
525
525
  def MA(cls):
526
526
  """Returns the link-out URI for objects of "Adult Mouse Anatomical Dictionary".
527
527
  """
528
- RDF::URI.new("http://www.informatics.jax.org/searches/AMA.cgi?id=MA:")
528
+ cls.Namespace("http://www.informatics.jax.org/searches/AMA.cgi?id=MA:")
529
529
 
530
530
  @classmethod
531
531
  def MaizeGDB(cls):
532
532
  """Returns the link-out URI for objects of "MaizeGDB".
533
533
  """
534
- RDF::URI.new("http://www.maizegdb.org/cgi-bin/id_search.cgi?id=")
534
+ cls.Namespace("http://www.maizegdb.org/cgi-bin/id_search.cgi?id=")
535
535
 
536
536
  @classmethod
537
537
  def MaizeGDB_Locus(cls):
538
538
  """Returns the link-out URI for objects of "MaizeGDB".
539
539
  """
540
- RDF::URI.new("http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=")
540
+ cls.Namespace("http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=")
541
541
 
542
542
  @classmethod
543
543
  def MEROPS(cls):
544
544
  """Returns the link-out URI for objects of "MEROPS peptidase database".
545
545
  """
546
- RDF::URI.new("http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=")
546
+ cls.Namespace("http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=")
547
547
 
548
548
  @classmethod
549
549
  def MEROPS_fam(cls):
550
550
  """Returns the link-out URI for objects of "MEROPS peptidase database".
551
551
  """
552
- RDF::URI.new("http://merops.sanger.ac.uk/cgi-bin/famsum?family=")
552
+ cls.Namespace("http://merops.sanger.ac.uk/cgi-bin/famsum?family=")
553
553
 
554
554
  @classmethod
555
555
  def MeSH(cls):
556
556
  """Returns the link-out URI for objects of "Medical Subject Headings".
557
557
  """
558
- RDF::URI.new("http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=")
558
+ cls.Namespace("http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=")
559
559
 
560
560
  @classmethod
561
561
  def MetaCyc(cls):
562
562
  """Returns the link-out URI for objects of "Metabolic Encyclopedia of metabolic and other pathways".
563
563
  """
564
- RDF::URI.new("http://biocyc.org/META/NEW-IMAGE?type=NIL&object=")
564
+ cls.Namespace("http://biocyc.org/META/NEW-IMAGE?type=NIL&object=")
565
565
 
566
566
  @classmethod
567
567
  def MGI(cls):
568
568
  """Returns the link-out URI for objects of "Mouse Genome Informatics".
569
569
  """
570
- RDF::URI.new("http://www.informatics.jax.org/accession/")
570
+ cls.Namespace("http://www.informatics.jax.org/accession/")
571
571
 
572
572
  @classmethod
573
573
  def MIPS_funcat(cls):
574
574
  """Returns the link-out URI for objects of "MIPS Functional Catalogue".
575
575
  """
576
- RDF::URI.new("http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=")
576
+ cls.Namespace("http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=")
577
577
 
578
578
  @classmethod
579
579
  def MO(cls):
580
580
  """Returns the link-out URI for objects of "MGED Ontology".
581
581
  """
582
- RDF::URI.new("http://mged.sourceforge.net/ontologies/MGEDontology.php#")
582
+ cls.Namespace("http://mged.sourceforge.net/ontologies/MGEDontology.php#")
583
583
 
584
584
  @classmethod
585
585
  def ModBase(cls):
586
586
  """Returns the link-out URI for objects of "ModBase comprehensive Database of Comparative Protein Structure Models".
587
587
  """
588
- RDF::URI.new("http://salilab.org/modbase/searchbyid?databaseID=")
588
+ cls.Namespace("http://salilab.org/modbase/searchbyid?databaseID=")
589
589
 
590
590
  @classmethod
591
591
  def NASC_code(cls):
592
592
  """Returns the link-out URI for objects of "Nottingham Arabidopsis Stock Centre Seeds Database".
593
593
  """
594
- RDF::URI.new("http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=")
594
+ cls.Namespace("http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=")
595
595
 
596
596
  @classmethod
597
597
  def NCBI_Gene(cls):
598
598
  """Returns the link-out URI for objects of "NCBI Gene".
599
599
  """
600
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=")
600
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=")
601
601
 
602
602
  @classmethod
603
603
  def NCBI_gi(cls):
604
604
  """Returns the link-out URI for objects of "NCBI databases".
605
605
  """
606
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
606
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
607
607
 
608
608
  @classmethod
609
609
  def NCBI_GP(cls):
610
610
  """Returns the link-out URI for objects of "NCBI GenPept".
611
611
  """
612
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=")
612
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=")
613
613
 
614
614
  @classmethod
615
615
  def NIF_Subcellular(cls):
616
616
  """Returns the link-out URI for objects of "Neuroscience Information Framework standard ontology, subcellular hierarchy".
617
617
  """
618
- RDF::URI.new("http://www.neurolex.org/wiki/")
618
+ cls.Namespace("http://www.neurolex.org/wiki/")
619
619
 
620
620
  @classmethod
621
621
  def NMPDR(cls):
622
622
  """Returns the link-out URI for objects of "National Microbial Pathogen Data Resource".
623
623
  """
624
- RDF::URI.new("http://www.nmpdr.org/linkin.cgi?id=")
624
+ cls.Namespace("http://www.nmpdr.org/linkin.cgi?id=")
625
625
 
626
626
  @classmethod
627
627
  def OMIM(cls):
628
628
  """Returns the link-out URI for objects of "Mendelian Inheritance in Man".
629
629
  """
630
- RDF::URI.new("http://omim.org/entry/")
630
+ cls.Namespace("http://omim.org/entry/")
631
631
 
632
632
  @classmethod
633
633
  def PAMGO_GAT(cls):
634
634
  """Returns the link-out URI for objects of "Genome Annotation Tool (cls, Agrobacterium tumefaciens C58); PAMGO Interest Group".
635
635
  """
636
- RDF::URI.new("http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=")
636
+ cls.Namespace("http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=")
637
637
 
638
638
  @classmethod
639
639
  def PAMGO_MGG(cls):
640
640
  """Returns the link-out URI for objects of "Magnaporthe grisea database".
641
641
  """
642
- RDF::URI.new("http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=")
642
+ cls.Namespace("http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=")
643
643
 
644
644
  @classmethod
645
645
  def PAMGO_VMD(cls):
646
646
  """Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
647
647
  """
648
- RDF::URI.new("http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=")
648
+ cls.Namespace("http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=")
649
649
 
650
650
  @classmethod
651
651
  def PANTHER(cls):
652
652
  """Returns the link-out URI for objects of "Protein ANalysis THrough Evolutionary Relationships".
653
653
  """
654
- RDF::URI.new("http://pantree.org/node/annotationNode.jsp?id=")
654
+ cls.Namespace("http://pantree.org/node/annotationNode.jsp?id=")
655
655
 
656
656
  @classmethod
657
657
  def PATRIC(cls):
658
658
  """Returns the link-out URI for objects of "PathoSystems Resource Integration Center".
659
659
  """
660
- RDF::URI.new("http://patric.vbi.vt.edu/gene/overview.php?fid=")
660
+ cls.Namespace("http://patric.vbi.vt.edu/gene/overview.php?fid=")
661
661
 
662
662
  @classmethod
663
663
  def PDB(cls):
664
664
  """Returns the link-out URI for objects of "Protein Data Bank".
665
665
  """
666
- RDF::URI.new("http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=")
666
+ cls.Namespace("http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=")
667
667
 
668
668
  @classmethod
669
669
  def Pfam(cls):
670
670
  """Returns the link-out URI for objects of "Pfam database of protein families".
671
671
  """
672
- RDF::URI.new("http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?")
672
+ cls.Namespace("http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?")
673
673
 
674
674
  @classmethod
675
675
  def PharmGKB(cls):
676
676
  """Returns the link-out URI for objects of "Pharmacogenetics and Pharmacogenomics Knowledge Base".
677
677
  """
678
- RDF::URI.new("http://www.pharmgkb.org/do/serve?objId=")
678
+ cls.Namespace("http://www.pharmgkb.org/do/serve?objId=")
679
679
 
680
680
  @classmethod
681
681
  def PIR(cls):
682
682
  """Returns the link-out URI for objects of "Protein Information Resource".
683
683
  """
684
- RDF::URI.new("http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=")
684
+ cls.Namespace("http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=")
685
685
 
686
686
  @classmethod
687
687
  def PIRSF(cls):
688
688
  """Returns the link-out URI for objects of "PIR Superfamily Classification System".
689
689
  """
690
- RDF::URI.new("http://pir.georgetown.edu/cgi-bin/ipcSF?id=")
690
+ cls.Namespace("http://pir.georgetown.edu/cgi-bin/ipcSF?id=")
691
691
 
692
692
  @classmethod
693
693
  def PMCID(cls):
694
694
  """Returns the link-out URI for objects of "Pubmed Central".
695
695
  """
696
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=")
696
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=")
697
697
 
698
698
  @classmethod
699
699
  def PMID(cls):
700
700
  """Returns the link-out URI for objects of "PubMed".
701
701
  """
702
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/pubmed/")
702
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/pubmed/")
703
703
 
704
704
  @classmethod
705
705
  def PO(cls):
706
706
  """Returns the link-out URI for objects of "Plant Ontology Consortium Database".
707
707
  """
708
- RDF::URI.new("http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:")
708
+ cls.Namespace("http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:")
709
709
 
710
710
  @classmethod
711
711
  def PO_REF(cls):
712
712
  """Returns the link-out URI for objects of "Plant Ontology custom references".
713
713
  """
714
- RDF::URI.new("http://wiki.plantontology.org:8080/index.php/PO_REF:")
714
+ cls.Namespace("http://wiki.plantontology.org:8080/index.php/PO_REF:")
715
715
 
716
716
  @classmethod
717
717
  def PomBase(cls):
718
718
  """Returns the link-out URI for objects of "PomBase".
719
719
  """
720
- RDF::URI.new("http://www.pombase.org/spombe/result/")
720
+ cls.Namespace("http://www.pombase.org/spombe/result/")
721
721
 
722
722
  @classmethod
723
723
  def PR(cls):
724
724
  """Returns the link-out URI for objects of "Protein Ontology".
725
725
  """
726
- RDF::URI.new("http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:")
726
+ cls.Namespace("http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:")
727
727
 
728
728
  @classmethod
729
729
  def PRINTS(cls):
730
730
  """Returns the link-out URI for objects of "PRINTS compendium of protein fingerprints".
731
731
  """
732
- RDF::URI.new("http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=False&regexpr=off&prints_accn=")
732
+ cls.Namespace("http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=False&regexpr=off&prints_accn=")
733
733
 
734
734
  @classmethod
735
735
  def ProDom(cls):
736
736
  """Returns the link-out URI for objects of "ProDom protein domain families".
737
737
  """
738
- RDF::URI.new("http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=")
738
+ cls.Namespace("http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=")
739
739
 
740
740
  @classmethod
741
741
  def Prosite(cls):
742
742
  """Returns the link-out URI for objects of "Prosite database of protein families and domains".
743
743
  """
744
- RDF::URI.new("http://www.expasy.ch/cgi-bin/prosite-search-ac?")
744
+ cls.Namespace("http://www.expasy.ch/cgi-bin/prosite-search-ac?")
745
745
 
746
746
  @classmethod
747
747
  def PseudoCAP(cls):
748
748
  """Returns the link-out URI for objects of "Pseudomonas Genome Project".
749
749
  """
750
- RDF::URI.new("http://v2.pseudomonas.com/getAnnotation.do?locusID=")
750
+ cls.Namespace("http://v2.pseudomonas.com/getAnnotation.do?locusID=")
751
751
 
752
752
  @classmethod
753
753
  def PSI_MOD(cls):
754
754
  """Returns the link-out URI for objects of "Proteomics Standards Initiative protein modification ontology".
755
755
  """
756
- RDF::URI.new("http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:")
756
+ cls.Namespace("http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:")
757
757
 
758
758
  @classmethod
759
759
  def PubChem_BioAssay(cls):
760
760
  """Returns the link-out URI for objects of "NCBI PubChem database of bioassay records".
761
761
  """
762
- RDF::URI.new("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=")
762
+ cls.Namespace("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=")
763
763
 
764
764
  @classmethod
765
765
  def PubChem_Compound(cls):
766
766
  """Returns the link-out URI for objects of "NCBI PubChem database of chemical structures".
767
767
  """
768
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=")
768
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=")
769
769
 
770
770
  @classmethod
771
771
  def PubChem_Substance(cls):
772
772
  """Returns the link-out URI for objects of "NCBI PubChem database of chemical substances".
773
773
  """
774
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=")
774
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=")
775
775
 
776
776
  @classmethod
777
777
  def Reactome(cls):
778
778
  """Returns the link-out URI for objects of "Reactome - a curated knowledgebase of biological pathways".
779
779
  """
780
- RDF::URI.new("http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=")
780
+ cls.Namespace("http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=")
781
781
 
782
782
  @classmethod
783
783
  def RefSeq(cls):
784
784
  """Returns the link-out URI for objects of "RefSeq".
785
785
  """
786
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
786
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
787
787
 
788
788
  @classmethod
789
789
  def RefSeq_NA(cls):
790
790
  """Returns the link-out URI for objects of "RefSeq (cls, Nucleic Acid)".
791
791
  """
792
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
792
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
793
793
 
794
794
  @classmethod
795
795
  def RefSeq_Prot(cls):
796
796
  """Returns the link-out URI for objects of "RefSeq (cls, Protein)".
797
797
  """
798
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
798
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
799
799
 
800
800
  @classmethod
801
801
  def Rfam(cls):
802
802
  """Returns the link-out URI for objects of "Rfam database of RNA families".
803
803
  """
804
- RDF::URI.new("http://rfam.sanger.ac.uk/family/")
804
+ cls.Namespace("http://rfam.sanger.ac.uk/family/")
805
805
 
806
806
  @classmethod
807
807
  def RGD(cls):
808
808
  """Returns the link-out URI for objects of "Rat Genome Database".
809
809
  """
810
- RDF::URI.new("http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=")
810
+ cls.Namespace("http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=")
811
811
 
812
812
  @classmethod
813
813
  def RHEA(cls):
814
814
  """Returns the link-out URI for objects of "Rhea, the Annotated Reactions Database".
815
815
  """
816
- RDF::URI.new("http://www.ebi.ac.uk/rhea/reaction.xhtml?id=")
816
+ cls.Namespace("http://www.ebi.ac.uk/rhea/reaction.xhtml?id=")
817
817
 
818
818
  @classmethod
819
819
  def RNAmods(cls):
820
820
  """Returns the link-out URI for objects of "RNA Modification Database".
821
821
  """
822
- RDF::URI.new("http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?")
822
+ cls.Namespace("http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?")
823
823
 
824
824
  @classmethod
825
825
  def RO(cls):
826
826
  """Returns the link-out URI for objects of "OBO Relation Ontology Ontology".
827
827
  """
828
- RDF::URI.new("http://purl.obolibrary.org/obo/RO_")
828
+ cls.Namespace("http://purl.obolibrary.org/obo/RO_")
829
829
 
830
830
  @classmethod
831
831
  def SABIO_RK(cls):
832
832
  """Returns the link-out URI for objects of "SABIO Reaction Kinetics".
833
833
  """
834
- RDF::URI.new("http://sabio.villa-bosch.de/reacdetails.jsp?reactid=")
834
+ cls.Namespace("http://sabio.villa-bosch.de/reacdetails.jsp?reactid=")
835
835
 
836
836
  @classmethod
837
837
  def SEED(cls):
838
838
  """Returns the link-out URI for objects of "The SEED;".
839
839
  """
840
- RDF::URI.new("http://www.theseed.org/linkin.cgi?id=")
840
+ cls.Namespace("http://www.theseed.org/linkin.cgi?id=")
841
841
 
842
842
  @classmethod
843
843
  def SGD(cls):
844
844
  """Returns the link-out URI for objects of "Saccharomyces Genome Database".
845
845
  """
846
- RDF::URI.new("http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=")
846
+ cls.Namespace("http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=")
847
847
 
848
848
  @classmethod
849
849
  def SGD_LOCUS(cls):
850
850
  """Returns the link-out URI for objects of "Saccharomyces Genome Database".
851
851
  """
852
- RDF::URI.new("http://db.yeastgenome.org/cgi-bin/locus.pl?locus=")
852
+ cls.Namespace("http://db.yeastgenome.org/cgi-bin/locus.pl?locus=")
853
853
 
854
854
  @classmethod
855
855
  def SGD_REF(cls):
856
856
  """Returns the link-out URI for objects of "Saccharomyces Genome Database".
857
857
  """
858
- RDF::URI.new("http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=")
858
+ cls.Namespace("http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=")
859
859
 
860
860
  @classmethod
861
861
  def SGN(cls):
862
862
  """Returns the link-out URI for objects of "Sol Genomics Network".
863
863
  """
864
- RDF::URI.new("http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=")
864
+ cls.Namespace("http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=")
865
865
 
866
866
  @classmethod
867
867
  def SGN_ref(cls):
868
868
  """Returns the link-out URI for objects of "Sol Genomics Network".
869
869
  """
870
- RDF::URI.new("http://www.sgn.cornell.edu/chado/publication.pl?pub_id=")
870
+ cls.Namespace("http://www.sgn.cornell.edu/chado/publication.pl?pub_id=")
871
871
 
872
872
  @classmethod
873
873
  def SMART(cls):
874
874
  """Returns the link-out URI for objects of "Simple Modular Architecture Research Tool".
875
875
  """
876
- RDF::URI.new("http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=")
876
+ cls.Namespace("http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=")
877
877
 
878
878
  @classmethod
879
879
  def SO(cls):
880
880
  """Returns the link-out URI for objects of "Sequence Ontology".
881
881
  """
882
- RDF::URI.new("http://song.sourceforge.net/SOterm_tables.html#SO:")
882
+ cls.Namespace("http://song.sourceforge.net/SOterm_tables.html#SO:")
883
883
 
884
884
  @classmethod
885
885
  def SUPERFAMILY(cls):
886
886
  """Returns the link-out URI for objects of "SUPERFAMILY protein annotation database".
887
887
  """
888
- RDF::URI.new("http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF")
888
+ cls.Namespace("http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF")
889
889
 
890
890
  @classmethod
891
891
  def Swiss_Prot(cls):
892
892
  """Returns the link-out URI for objects of "UniProtKB/Swiss-Prot".
893
893
  """
894
- RDF::URI.new("http://www.uniprot.org/uniprot/")
894
+ cls.Namespace("http://www.uniprot.org/uniprot/")
895
895
 
896
896
  @classmethod
897
897
  def TAIR(cls):
898
898
  """Returns the link-out URI for objects of "The Arabidopsis Information Resource".
899
899
  """
900
- RDF::URI.new("http://arabidopsis.org/servlets/TairObject?accession=")
900
+ cls.Namespace("http://arabidopsis.org/servlets/TairObject?accession=")
901
901
 
902
902
  @classmethod
903
903
  def taxon(cls):
904
904
  """Returns the link-out URI for objects of "NCBI Taxonomy".
905
905
  """
906
- RDF::URI.new("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=")
906
+ cls.Namespace("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=")
907
907
 
908
908
  @classmethod
909
909
  def TC(cls):
910
910
  """Returns the link-out URI for objects of "Transport Protein Database".
911
911
  """
912
- RDF::URI.new("http://www.tcdb.org/tcdb/index.php?tc=")
912
+ cls.Namespace("http://www.tcdb.org/tcdb/index.php?tc=")
913
913
 
914
914
  @classmethod
915
915
  def TGD_LOCUS(cls):
916
916
  """Returns the link-out URI for objects of "Tetrahymena Genome Database".
917
917
  """
918
- RDF::URI.new("http://db.ciliate.org/cgi-bin/locus.pl?locus=")
918
+ cls.Namespace("http://db.ciliate.org/cgi-bin/locus.pl?locus=")
919
919
 
920
920
  @classmethod
921
921
  def TGD_REF(cls):
922
922
  """Returns the link-out URI for objects of "Tetrahymena Genome Database".
923
923
  """
924
- RDF::URI.new("http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=")
924
+ cls.Namespace("http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=")
925
925
 
926
926
  @classmethod
927
927
  def TrEMBL(cls):
928
928
  """Returns the link-out URI for objects of "UniProtKB-TrEMBL protein sequence database".
929
929
  """
930
- RDF::URI.new("http://www.uniprot.org/uniprot/")
930
+ cls.Namespace("http://www.uniprot.org/uniprot/")
931
931
 
932
932
  @classmethod
933
933
  def UBERON(cls):
934
934
  """Returns the link-out URI for objects of "Uber-anatomy ontology".
935
935
  """
936
- RDF::URI.new("http://purl.obolibrary.org/obo/UBERON_")
936
+ cls.Namespace("http://purl.obolibrary.org/obo/UBERON_")
937
937
 
938
938
  @classmethod
939
939
  def UM_BBD_enzymeID(cls):
940
940
  """Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
941
941
  """
942
- RDF::URI.new("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=")
942
+ cls.Namespace("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=")
943
943
 
944
944
  @classmethod
945
945
  def UM_BBD_reactionID(cls):
946
946
  """Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
947
947
  """
948
- RDF::URI.new("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=")
948
+ cls.Namespace("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=")
949
949
 
950
950
  @classmethod
951
951
  def UM_BBD_ruleID(cls):
952
952
  """Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
953
953
  """
954
- RDF::URI.new("http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=")
954
+ cls.Namespace("http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=")
955
955
 
956
956
  @classmethod
957
957
  def UniMod(cls):
958
958
  """Returns the link-out URI for objects of "UniMod".
959
959
  """
960
- RDF::URI.new("http://www.unimod.org/modifications_view.php?editid1=")
960
+ cls.Namespace("http://www.unimod.org/modifications_view.php?editid1=")
961
961
 
962
962
  @classmethod
963
963
  def UniParc(cls):
964
964
  """Returns the link-out URI for objects of "UniProt Archive".
965
965
  """
966
- RDF::URI.new("http://www.uniprot.org/uniparc/")
966
+ cls.Namespace("http://www.uniprot.org/uniparc/")
967
967
 
968
968
  @classmethod
969
969
  def UniPathway(cls):
970
970
  """Returns the link-out URI for objects of "UniPathway".
971
971
  """
972
- RDF::URI.new("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=")
972
+ cls.Namespace("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=")
973
973
 
974
974
  @classmethod
975
975
  def UniProtKB(cls):
976
976
  """Returns the link-out URI for objects of "Universal Protein Knowledgebase".
977
977
  """
978
- RDF::URI.new("http://www.uniprot.org/uniprot/")
978
+ cls.Namespace("http://www.uniprot.org/uniprot/")
979
979
 
980
980
  @classmethod
981
981
  def UniProtKB_KW(cls):
982
982
  """Returns the link-out URI for objects of "UniProt Knowledgebase keywords".
983
983
  """
984
- RDF::URI.new("http://www.uniprot.org/keywords/")
984
+ cls.Namespace("http://www.uniprot.org/keywords/")
985
985
 
986
986
  @classmethod
987
987
  def UniProtKB_SubCell(cls):
988
988
  """Returns the link-out URI for objects of "UniProt Knowledgebase Subcellular Location vocabulary".
989
989
  """
990
- RDF::URI.new("http://www.uniprot.org/locations/")
990
+ cls.Namespace("http://www.uniprot.org/locations/")
991
991
 
992
992
  @classmethod
993
993
  def VBRC(cls):
994
994
  """Returns the link-out URI for objects of "Viral Bioinformatics Resource Center".
995
995
  """
996
- RDF::URI.new("http://vbrc.org/query.asp?web_id=VBRC:")
996
+ cls.Namespace("http://vbrc.org/query.asp?web_id=VBRC:")
997
997
 
998
998
  @classmethod
999
999
  def VEGA(cls):
1000
1000
  """Returns the link-out URI for objects of "Vertebrate Genome Annotation database".
1001
1001
  """
1002
- RDF::URI.new("http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=")
1002
+ cls.Namespace("http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=")
1003
1003
 
1004
1004
  @classmethod
1005
1005
  def VMD(cls):
1006
1006
  """Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
1007
1007
  """
1008
- RDF::URI.new("http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=")
1008
+ cls.Namespace("http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=")
1009
1009
 
1010
1010
  @classmethod
1011
1011
  def WB(cls):
1012
1012
  """Returns the link-out URI for objects of "WormBase database of nematode biology".
1013
1013
  """
1014
- RDF::URI.new("http://www.wormbase.org/db/gene/gene?name=")
1014
+ cls.Namespace("http://www.wormbase.org/db/gene/gene?name=")
1015
1015
 
1016
1016
  @classmethod
1017
1017
  def WB_REF(cls):
1018
1018
  """Returns the link-out URI for objects of "WormBase database of nematode biology".
1019
1019
  """
1020
- RDF::URI.new("http://www.wormbase.org/db/misc/paper?name=")
1020
+ cls.Namespace("http://www.wormbase.org/db/misc/paper?name=")
1021
1021
 
1022
1022
  @classmethod
1023
1023
  def Wikipedia(cls):
1024
1024
  """Returns the link-out URI for objects of "Wikipedia".
1025
1025
  """
1026
- RDF::URI.new("http://en.wikipedia.org/wiki/")
1026
+ cls.Namespace("http://en.wikipedia.org/wiki/")
1027
1027
 
1028
1028
  @classmethod
1029
1029
  def WP(cls):
1030
1030
  """Returns the link-out URI for objects of "Wormpep database of proteins of C. elegans".
1031
1031
  """
1032
- RDF::URI.new("http://www.wormbase.org/db/get?class=Protein;name=WP:")
1032
+ cls.Namespace("http://www.wormbase.org/db/get?class=Protein;name=WP:")
1033
1033
 
1034
1034
  @classmethod
1035
1035
  def ZFIN(cls):
1036
1036
  """Returns the link-out URI for objects of "Zebrafish Information Network".
1037
1037
  """
1038
- RDF::URI.new("http://zfin.org/cgi-bin/ZFIN_jump?record=")
1038
+ cls.Namespace("http://zfin.org/cgi-bin/ZFIN_jump?record=")
1039
1039
 
1040
1040