biointerchange 0.2.2 → 1.0.0

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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
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  """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
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  @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