bio-publisci 0.0.8 → 0.1.0

Sign up to get free protection for your applications and to get access to all the features.
Files changed (94) hide show
  1. checksums.yaml +7 -0
  2. data/Gemfile +10 -0
  3. data/Rakefile +1 -1
  4. data/bin/bio-publisci-server +50 -0
  5. data/features/reader_steps.rb +1 -1
  6. data/lib/bio-publisci.rb +11 -2
  7. data/lib/bio-publisci/datacube_model.rb +92 -88
  8. data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +0 -1
  9. data/lib/bio-publisci/dataset/data_cube.rb +78 -44
  10. data/lib/bio-publisci/dataset/dataset_for.rb +26 -27
  11. data/lib/bio-publisci/metadata/metadata_model.rb +21 -23
  12. data/lib/bio-publisci/metadata/prov/model/prov_models.rb +5 -5
  13. data/lib/bio-publisci/output.rb +1 -1
  14. data/lib/bio-publisci/parser.rb +130 -12
  15. data/lib/bio-publisci/post_processor.rb +95 -0
  16. data/lib/bio-publisci/query/query_helper.rb +13 -8
  17. data/lib/bio-publisci/readers/arff.rb +1 -1
  18. data/lib/bio-publisci/readers/base.rb +57 -0
  19. data/lib/bio-publisci/readers/csv.rb +2 -5
  20. data/lib/bio-publisci/readers/dataframe.rb +2 -2
  21. data/lib/bio-publisci/readers/maf.rb +199 -0
  22. data/lib/bio-publisci/readers/r_cross.rb +6 -10
  23. data/lib/bio-publisci/readers/r_matrix.rb +1 -1
  24. data/lib/bio-publisci/writers/base.rb +16 -0
  25. data/lib/bio-publisci/writers/json.rb +18 -0
  26. data/resources/maf_example.maf +10 -0
  27. data/resources/maf_rdf.ttl +1173 -0
  28. data/resources/primer.ttl +38 -0
  29. data/resources/queries/gene.rq +16 -0
  30. data/resources/queries/hugo_to_ensembl.rq +7 -0
  31. data/resources/queries/maf_column.rq +26 -0
  32. data/resources/queries/patient.rq +11 -0
  33. data/resources/queries/patient_list.rq +11 -0
  34. data/resources/queries/patients_with_mutation.rq +18 -0
  35. data/scripts/get_gene_lengths.rb +50 -0
  36. data/scripts/islet_mlratio.rb +1 -1
  37. data/scripts/scan_islet.rb +1 -1
  38. data/scripts/update_reference.rb +8 -3
  39. data/server/helpers.rb +215 -0
  40. data/server/public/src-min-noconflict/LICENSE +24 -0
  41. data/server/public/src-min-noconflict/ace.js +11 -0
  42. data/server/public/src-min-noconflict/ext-chromevox.js +1 -0
  43. data/server/public/src-min-noconflict/ext-elastic_tabstops_lite.js +1 -0
  44. data/server/public/src-min-noconflict/ext-emmet.js +1 -0
  45. data/server/public/src-min-noconflict/ext-keybinding_menu.js +1 -0
  46. data/server/public/src-min-noconflict/ext-language_tools.js +1 -0
  47. data/server/public/src-min-noconflict/ext-modelist.js +1 -0
  48. data/server/public/src-min-noconflict/ext-old_ie.js +1 -0
  49. data/server/public/src-min-noconflict/ext-searchbox.js +1 -0
  50. data/server/public/src-min-noconflict/ext-settings_menu.js +1 -0
  51. data/server/public/src-min-noconflict/ext-spellcheck.js +1 -0
  52. data/server/public/src-min-noconflict/ext-split.js +1 -0
  53. data/server/public/src-min-noconflict/ext-static_highlight.js +1 -0
  54. data/server/public/src-min-noconflict/ext-statusbar.js +1 -0
  55. data/server/public/src-min-noconflict/ext-textarea.js +1 -0
  56. data/server/public/src-min-noconflict/ext-themelist.js +1 -0
  57. data/server/public/src-min-noconflict/ext-whitespace.js +1 -0
  58. data/server/public/src-min-noconflict/keybinding-emacs.js +1 -0
  59. data/server/public/src-min-noconflict/keybinding-vim.js +1 -0
  60. data/server/public/src-min-noconflict/mode-ruby.js +1 -0
  61. data/server/public/src-min-noconflict/snippets/ruby.js +1 -0
  62. data/server/public/src-min-noconflict/theme-twilight.js +1 -0
  63. data/server/public/src-min-noconflict/worker-coffee.js +1 -0
  64. data/server/public/src-min-noconflict/worker-css.js +1 -0
  65. data/server/public/src-min-noconflict/worker-javascript.js +1 -0
  66. data/server/public/src-min-noconflict/worker-json.js +1 -0
  67. data/server/public/src-min-noconflict/worker-lua.js +1 -0
  68. data/server/public/src-min-noconflict/worker-php.js +1 -0
  69. data/server/public/src-min-noconflict/worker-xquery.js +1 -0
  70. data/server/routes.rb +123 -0
  71. data/server/views/dsl.haml +65 -0
  72. data/server/views/dump.haml +3 -0
  73. data/server/views/import.haml +35 -0
  74. data/server/views/new_repository.haml +25 -0
  75. data/server/views/query.haml +28 -0
  76. data/server/views/repository.haml +25 -0
  77. data/spec/ORM/data_cube_orm_spec.rb +1 -0
  78. data/spec/bnode_spec.rb +66 -0
  79. data/spec/data_cube_spec.rb +66 -63
  80. data/spec/dataset_for_spec.rb +36 -16
  81. data/spec/dsl_spec.rb +41 -0
  82. data/spec/generators/csv_spec.rb +3 -3
  83. data/spec/generators/dataframe_spec.rb +2 -2
  84. data/spec/generators/maf_spec.rb +40 -0
  85. data/spec/generators/r_cross_spec.rb +2 -2
  86. data/spec/generators/r_matrix_spec.rb +2 -2
  87. data/spec/length_lookup_spec.rb +0 -0
  88. data/spec/maf_query_spec.rb +343 -0
  89. data/spec/resource/example.Rhistory +1 -1
  90. data/spec/turtle/bacon +9 -9
  91. data/spec/turtle/reference +43 -43
  92. data/spec/turtle/weather +10 -10
  93. data/spec/writer_spec.rb +16 -2
  94. metadata +212 -61
data/resources/maf_rdf.ttl ADDED
@@ -0,0 +1,1173 @@
1
+ @base <http://onto.strinz.me/dc/dataset/maf_example/> .
2
+ @prefix ns: <http://onto.strinz.me/dc/dataset/maf_example/> .
3
+ @prefix qb: <http://purl.org/linked-data/cube#> .
4
+ @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
5
+ @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
6
+ @prefix prop: <http://onto.strinz.me/properties/> .
7
+ @prefix dct: <http://purl.org/dc/terms/> .
8
+ @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
9
+ @prefix cs: <http://onto.strinz.me/dc/dataset/maf_example/cs/> .
10
+ @prefix code: <http://onto.strinz.me/dc/dataset/maf_example/code/> .
11
+ @prefix owl: <http://www.w3.org/2002/07/owl#> .
12
+ @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
13
+ @prefix foaf: <http://xmlns.com/foaf/0.1/> .
14
+ @prefix org: <http://www.w3.org/ns/org#> .
15
+ @prefix prov: <http://www.w3.org/ns/prov#> .
16
+
17
+ ns:dsd-maf_example a qb:DataStructureDefinition;
18
+ qb:component cs:Variant_Classification ;
19
+ qb:component cs:Variant_Type ;
20
+ qb:component cs:dbSNP_Val_Status ;
21
+ qb:component cs:Verification_Status ;
22
+ qb:component cs:Validation_Status ;
23
+ qb:component cs:Mutation_Status ;
24
+ qb:component cs:Sequence_Source ;
25
+ qb:component cs:Sequencer ;
26
+ qb:component cs:Hugo_Symbol ;
27
+ qb:component cs:Entrez_Gene_Id ;
28
+ qb:component cs:Center ;
29
+ qb:component cs:NCBI_Build ;
30
+ qb:component cs:Chromosome ;
31
+ qb:component cs:Start_Position ;
32
+ qb:component cs:End_Position ;
33
+ qb:component cs:Strand ;
34
+ qb:component cs:Reference_Allele ;
35
+ qb:component cs:Tumor_Seq_Allele1 ;
36
+ qb:component cs:Tumor_Seq_Allele2 ;
37
+ qb:component cs:dbSNP_RS ;
38
+ qb:component cs:Tumor_Sample_Barcode ;
39
+ qb:component cs:Matched_Norm_Sample_Barcode ;
40
+ qb:component cs:Match_Norm_Seq_Allele1 ;
41
+ qb:component cs:Match_Norm_Seq_Allele2 ;
42
+ qb:component cs:Tumor_Validation_Allele1 ;
43
+ qb:component cs:Tumor_Validation_Allele2 ;
44
+ qb:component cs:Match_Norm_Validation_Allele1 ;
45
+ qb:component cs:Match_Norm_Validation_Allele2 ;
46
+ qb:component cs:Sequencing_Phase ;
47
+ qb:component cs:Validation_Method ;
48
+ qb:component cs:Score ;
49
+ qb:component cs:BAM_File ;
50
+ qb:component cs:Tumor_Sample_UUID ;
51
+ qb:component cs:Matched_Norm_Sample_UUID ;
52
+ qb:component cs:patient_id ;
53
+ qb:component cs:sample_id .
54
+
55
+ ns:dataset-maf_example a qb:DataSet ;
56
+ rdfs:label "maf_example"@en ;
57
+ qb:structure ns:dsd-maf_example .
58
+
59
+ cs:Variant_Classification a qb:ComponentSpecification ;
60
+ rdfs:label "Variant_Classification" ;
61
+ qb:dimension prop:Variant_Classification .
62
+
63
+ cs:Variant_Type a qb:ComponentSpecification ;
64
+ rdfs:label "Variant_Type" ;
65
+ qb:dimension prop:Variant_Type .
66
+
67
+ cs:dbSNP_Val_Status a qb:ComponentSpecification ;
68
+ rdfs:label "dbSNP_Val_Status" ;
69
+ qb:dimension prop:dbSNP_Val_Status .
70
+
71
+ cs:Verification_Status a qb:ComponentSpecification ;
72
+ rdfs:label "Verification_Status" ;
73
+ qb:dimension prop:Verification_Status .
74
+
75
+ cs:Validation_Status a qb:ComponentSpecification ;
76
+ rdfs:label "Validation_Status" ;
77
+ qb:dimension prop:Validation_Status .
78
+
79
+ cs:Mutation_Status a qb:ComponentSpecification ;
80
+ rdfs:label "Mutation_Status" ;
81
+ qb:dimension prop:Mutation_Status .
82
+
83
+ cs:Sequence_Source a qb:ComponentSpecification ;
84
+ rdfs:label "Sequence_Source" ;
85
+ qb:dimension prop:Sequence_Source .
86
+
87
+ cs:Sequencer a qb:ComponentSpecification ;
88
+ rdfs:label "Sequencer" ;
89
+ qb:dimension prop:Sequencer .
90
+
91
+ cs:Hugo_Symbol a qb:ComponentSpecification ;
92
+ rdfs:label "Hugo_Symbol" ;
93
+ qb:measure prop:Hugo_Symbol .
94
+
95
+ cs:Entrez_Gene_Id a qb:ComponentSpecification ;
96
+ rdfs:label "Entrez_Gene_Id" ;
97
+ qb:measure prop:Entrez_Gene_Id .
98
+
99
+ cs:Center a qb:ComponentSpecification ;
100
+ rdfs:label "Center" ;
101
+ qb:measure prop:Center .
102
+
103
+ cs:NCBI_Build a qb:ComponentSpecification ;
104
+ rdfs:label "NCBI_Build" ;
105
+ qb:measure prop:NCBI_Build .
106
+
107
+ cs:Chromosome a qb:ComponentSpecification ;
108
+ rdfs:label "Chromosome" ;
109
+ qb:measure prop:Chromosome .
110
+
111
+ cs:Start_Position a qb:ComponentSpecification ;
112
+ rdfs:label "Start_Position" ;
113
+ qb:measure prop:Start_Position .
114
+
115
+ cs:End_Position a qb:ComponentSpecification ;
116
+ rdfs:label "End_Position" ;
117
+ qb:measure prop:End_Position .
118
+
119
+ cs:Strand a qb:ComponentSpecification ;
120
+ rdfs:label "Strand" ;
121
+ qb:measure prop:Strand .
122
+
123
+ cs:Reference_Allele a qb:ComponentSpecification ;
124
+ rdfs:label "Reference_Allele" ;
125
+ qb:measure prop:Reference_Allele .
126
+
127
+ cs:Tumor_Seq_Allele1 a qb:ComponentSpecification ;
128
+ rdfs:label "Tumor_Seq_Allele1" ;
129
+ qb:measure prop:Tumor_Seq_Allele1 .
130
+
131
+ cs:Tumor_Seq_Allele2 a qb:ComponentSpecification ;
132
+ rdfs:label "Tumor_Seq_Allele2" ;
133
+ qb:measure prop:Tumor_Seq_Allele2 .
134
+
135
+ cs:dbSNP_RS a qb:ComponentSpecification ;
136
+ rdfs:label "dbSNP_RS" ;
137
+ qb:measure prop:dbSNP_RS .
138
+
139
+ cs:Tumor_Sample_Barcode a qb:ComponentSpecification ;
140
+ rdfs:label "Tumor_Sample_Barcode" ;
141
+ qb:measure prop:Tumor_Sample_Barcode .
142
+
143
+ cs:Matched_Norm_Sample_Barcode a qb:ComponentSpecification ;
144
+ rdfs:label "Matched_Norm_Sample_Barcode" ;
145
+ qb:measure prop:Matched_Norm_Sample_Barcode .
146
+
147
+ cs:Match_Norm_Seq_Allele1 a qb:ComponentSpecification ;
148
+ rdfs:label "Match_Norm_Seq_Allele1" ;
149
+ qb:measure prop:Match_Norm_Seq_Allele1 .
150
+
151
+ cs:Match_Norm_Seq_Allele2 a qb:ComponentSpecification ;
152
+ rdfs:label "Match_Norm_Seq_Allele2" ;
153
+ qb:measure prop:Match_Norm_Seq_Allele2 .
154
+
155
+ cs:Tumor_Validation_Allele1 a qb:ComponentSpecification ;
156
+ rdfs:label "Tumor_Validation_Allele1" ;
157
+ qb:measure prop:Tumor_Validation_Allele1 .
158
+
159
+ cs:Tumor_Validation_Allele2 a qb:ComponentSpecification ;
160
+ rdfs:label "Tumor_Validation_Allele2" ;
161
+ qb:measure prop:Tumor_Validation_Allele2 .
162
+
163
+ cs:Match_Norm_Validation_Allele1 a qb:ComponentSpecification ;
164
+ rdfs:label "Match_Norm_Validation_Allele1" ;
165
+ qb:measure prop:Match_Norm_Validation_Allele1 .
166
+
167
+ cs:Match_Norm_Validation_Allele2 a qb:ComponentSpecification ;
168
+ rdfs:label "Match_Norm_Validation_Allele2" ;
169
+ qb:measure prop:Match_Norm_Validation_Allele2 .
170
+
171
+ cs:Sequencing_Phase a qb:ComponentSpecification ;
172
+ rdfs:label "Sequencing_Phase" ;
173
+ qb:measure prop:Sequencing_Phase .
174
+
175
+ cs:Validation_Method a qb:ComponentSpecification ;
176
+ rdfs:label "Validation_Method" ;
177
+ qb:measure prop:Validation_Method .
178
+
179
+ cs:Score a qb:ComponentSpecification ;
180
+ rdfs:label "Score" ;
181
+ qb:measure prop:Score .
182
+
183
+ cs:BAM_File a qb:ComponentSpecification ;
184
+ rdfs:label "BAM_File" ;
185
+ qb:measure prop:BAM_File .
186
+
187
+ cs:Tumor_Sample_UUID a qb:ComponentSpecification ;
188
+ rdfs:label "Tumor_Sample_UUID" ;
189
+ qb:measure prop:Tumor_Sample_UUID .
190
+
191
+ cs:Matched_Norm_Sample_UUID a qb:ComponentSpecification ;
192
+ rdfs:label "Matched_Norm_Sample_UUID" ;
193
+ qb:measure prop:Matched_Norm_Sample_UUID .
194
+
195
+ cs:patient_id a qb:ComponentSpecification ;
196
+ rdfs:label "patient_id" ;
197
+ qb:measure prop:patient_id .
198
+
199
+ cs:sample_id a qb:ComponentSpecification ;
200
+ rdfs:label "sample_id" ;
201
+ qb:measure prop:sample_id .
202
+
203
+ prop:Hugo_Symbol a rdf:Property, qb:MeasureProperty ;
204
+ rdfs:label "Hugo_Symbol"@en .
205
+
206
+ prop:Entrez_Gene_Id a rdf:Property, qb:MeasureProperty ;
207
+ rdfs:label "Entrez_Gene_Id"@en .
208
+
209
+ prop:Center a rdf:Property, qb:MeasureProperty ;
210
+ rdfs:label "Center"@en ;
211
+ rdfs:range xsd:string .
212
+
213
+ prop:NCBI_Build a rdf:Property, qb:MeasureProperty ;
214
+ rdfs:label "NCBI_Build"@en ;
215
+ rdfs:range xsd:int .
216
+
217
+ prop:Chromosome a rdf:Property, qb:MeasureProperty ;
218
+ rdfs:label "Chromosome"@en ;
219
+ rdfs:range xsd:int .
220
+
221
+ prop:Start_Position a rdf:Property, qb:MeasureProperty ;
222
+ rdfs:label "Start_Position"@en .
223
+
224
+ prop:End_Position a rdf:Property, qb:MeasureProperty ;
225
+ rdfs:label "End_Position"@en .
226
+
227
+ prop:Strand a rdf:Property, qb:MeasureProperty ;
228
+ rdfs:label "Strand"@en .
229
+
230
+ prop:Reference_Allele a rdf:Property, qb:MeasureProperty ;
231
+ rdfs:label "Reference_Allele"@en .
232
+
233
+ prop:Tumor_Seq_Allele1 a rdf:Property, qb:MeasureProperty ;
234
+ rdfs:label "Tumor_Seq_Allele1"@en .
235
+
236
+ prop:Tumor_Seq_Allele2 a rdf:Property, qb:MeasureProperty ;
237
+ rdfs:label "Tumor_Seq_Allele2"@en .
238
+
239
+ prop:dbSNP_RS a rdf:Property, qb:MeasureProperty ;
240
+ rdfs:label "dbSNP_RS"@en .
241
+
242
+ prop:Tumor_Sample_Barcode a rdf:Property, qb:MeasureProperty ;
243
+ rdfs:label "Tumor_Sample_Barcode"@en ;
244
+ rdfs:range xsd:string .
245
+
246
+ prop:Matched_Norm_Sample_Barcode a rdf:Property, qb:MeasureProperty ;
247
+ rdfs:label "Matched_Norm_Sample_Barcode"@en .
248
+
249
+ prop:Match_Norm_Seq_Allele1 a rdf:Property, qb:MeasureProperty ;
250
+ rdfs:label "Match_Norm_Seq_Allele1"@en .
251
+
252
+ prop:Match_Norm_Seq_Allele2 a rdf:Property, qb:MeasureProperty ;
253
+ rdfs:label "Match_Norm_Seq_Allele2"@en .
254
+
255
+ prop:Tumor_Validation_Allele1 a rdf:Property, qb:MeasureProperty ;
256
+ rdfs:label "Tumor_Validation_Allele1"@en .
257
+
258
+ prop:Tumor_Validation_Allele2 a rdf:Property, qb:MeasureProperty ;
259
+ rdfs:label "Tumor_Validation_Allele2"@en .
260
+
261
+ prop:Match_Norm_Validation_Allele1 a rdf:Property, qb:MeasureProperty ;
262
+ rdfs:label "Match_Norm_Validation_Allele1"@en .
263
+
264
+ prop:Match_Norm_Validation_Allele2 a rdf:Property, qb:MeasureProperty ;
265
+ rdfs:label "Match_Norm_Validation_Allele2"@en .
266
+
267
+ prop:Sequencing_Phase a rdf:Property, qb:MeasureProperty ;
268
+ rdfs:label "Sequencing_Phase"@en .
269
+
270
+ prop:Validation_Method a rdf:Property, qb:MeasureProperty ;
271
+ rdfs:label "Validation_Method"@en .
272
+
273
+ prop:Score a rdf:Property, qb:MeasureProperty ;
274
+ rdfs:label "Score"@en .
275
+
276
+ prop:BAM_File a rdf:Property, qb:MeasureProperty ;
277
+ rdfs:label "BAM_File"@en .
278
+
279
+ prop:Tumor_Sample_UUID a rdf:Property, qb:MeasureProperty ;
280
+ rdfs:label "Tumor_Sample_UUID"@en .
281
+
282
+ prop:Matched_Norm_Sample_UUID a rdf:Property, qb:MeasureProperty ;
283
+ rdfs:label "Matched_Norm_Sample_UUID"@en .
284
+
285
+ prop:patient_id a rdf:Property, qb:MeasureProperty ;
286
+ rdfs:label "patient_id"@en .
287
+
288
+ prop:sample_id a rdf:Property, qb:MeasureProperty ;
289
+ rdfs:label "sample_id"@en .
290
+
291
+ prop:Variant_Classification a rdf:Property, qb:DimensionProperty ;
292
+ rdfs:label "Variant_Classification"@en ;
293
+ qb:codeList code:variant_classification ;
294
+ rdfs:range code:Variant_classification .
295
+
296
+ prop:Variant_Type a rdf:Property, qb:DimensionProperty ;
297
+ rdfs:label "Variant_Type"@en ;
298
+ qb:codeList code:variant_type ;
299
+ rdfs:range code:Variant_type .
300
+
301
+ prop:dbSNP_Val_Status a rdf:Property, qb:DimensionProperty ;
302
+ rdfs:label "dbSNP_Val_Status"@en ;
303
+ qb:codeList code:dbsnp_val_status ;
304
+ rdfs:range code:Dbsnp_val_status .
305
+
306
+ prop:Verification_Status a rdf:Property, qb:DimensionProperty ;
307
+ rdfs:label "Verification_Status"@en ;
308
+ qb:codeList code:verification_status ;
309
+ rdfs:range code:Verification_status .
310
+
311
+ prop:Validation_Status a rdf:Property, qb:DimensionProperty ;
312
+ rdfs:label "Validation_Status"@en ;
313
+ qb:codeList code:validation_status ;
314
+ rdfs:range code:Validation_status .
315
+
316
+ prop:Mutation_Status a rdf:Property, qb:DimensionProperty ;
317
+ rdfs:label "Mutation_Status"@en ;
318
+ qb:codeList code:mutation_status ;
319
+ rdfs:range code:Mutation_status .
320
+
321
+ prop:Sequence_Source a rdf:Property, qb:DimensionProperty ;
322
+ rdfs:label "Sequence_Source"@en ;
323
+ qb:codeList code:sequence_source ;
324
+ rdfs:range code:Sequence_source .
325
+
326
+ prop:Sequencer a rdf:Property, qb:DimensionProperty ;
327
+ rdfs:label "Sequencer"@en ;
328
+ qb:codeList code:sequencer ;
329
+ rdfs:range code:Sequencer .
330
+
331
+ code:Variant_classification a rdfs:Class, owl:Class;
332
+ rdfs:subClassOf skos:Concept ;
333
+ rdfs:label "Code list for variant_classification - codelist class"@en;
334
+ rdfs:comment "Specifies the variant_classification for each observation";
335
+ rdfs:seeAlso code:variant_classification .
336
+
337
+ code:variant_classification a skos:ConceptScheme;
338
+ skos:prefLabel "Code list for variant_classification - codelist scheme"@en;
339
+ rdfs:label "Code list for variant_classification - codelist scheme"@en;
340
+ skos:notation "CL_VARIANT_CLASSIFICATION";
341
+ skos:note "Specifies the variant_classification for each observation";
342
+ skos:hasTopConcept <code/variant_classification/Frame_Shift_Del> ;
343
+ skos:hasTopConcept <code/variant_classification/Frame_Shift_Ins> ;
344
+ skos:hasTopConcept <code/variant_classification/In_Frame_Del> ;
345
+ skos:hasTopConcept <code/variant_classification/In_Frame_Ins> ;
346
+ skos:hasTopConcept <code/variant_classification/Missense_Mutation> ;
347
+ skos:hasTopConcept <code/variant_classification/Nonsense_Mutation> ;
348
+ skos:hasTopConcept <code/variant_classification/Silent> ;
349
+ skos:hasTopConcept <code/variant_classification/Splice_Site> ;
350
+ skos:hasTopConcept <code/variant_classification/Translation_Start_Site> ;
351
+ skos:hasTopConcept <code/variant_classification/Nonstop_Mutation> ;
352
+ skos:hasTopConcept <code/variant_classification/3'UTR> ;
353
+ skos:hasTopConcept <code/variant_classification/3'Flank> ;
354
+ skos:hasTopConcept <code/variant_classification/5'UTR> ;
355
+ skos:hasTopConcept <code/variant_classification/5'Flank> ;
356
+ skos:hasTopConcept <code/variant_classification/IGR1> ;
357
+ skos:hasTopConcept <code/variant_classification/Intron> ;
358
+ skos:hasTopConcept <code/variant_classification/RNA> ;
359
+ skos:hasTopConcept <code/variant_classification/Targeted_Region> ;
360
+ .
361
+
362
+ code:Variant_type a rdfs:Class, owl:Class;
363
+ rdfs:subClassOf skos:Concept ;
364
+ rdfs:label "Code list for variant_type - codelist class"@en;
365
+ rdfs:comment "Specifies the variant_type for each observation";
366
+ rdfs:seeAlso code:variant_type .
367
+
368
+ code:variant_type a skos:ConceptScheme;
369
+ skos:prefLabel "Code list for variant_type - codelist scheme"@en;
370
+ rdfs:label "Code list for variant_type - codelist scheme"@en;
371
+ skos:notation "CL_VARIANT_TYPE";
372
+ skos:note "Specifies the variant_type for each observation";
373
+ skos:hasTopConcept <code/variant_type/SNP> ;
374
+ skos:hasTopConcept <code/variant_type/DNP> ;
375
+ skos:hasTopConcept <code/variant_type/TNP> ;
376
+ skos:hasTopConcept <code/variant_type/ONP> ;
377
+ skos:hasTopConcept <code/variant_type/INS> ;
378
+ skos:hasTopConcept <code/variant_type/DEL> ;
379
+ skos:hasTopConcept <code/variant_type/Consolidated> ;
380
+ .
381
+
382
+ code:Dbsnp_val_status a rdfs:Class, owl:Class;
383
+ rdfs:subClassOf skos:Concept ;
384
+ rdfs:label "Code list for dbsnp_val_status - codelist class"@en;
385
+ rdfs:comment "Specifies the dbsnp_val_status for each observation";
386
+ rdfs:seeAlso code:dbsnp_val_status .
387
+
388
+ code:dbsnp_val_status a skos:ConceptScheme;
389
+ skos:prefLabel "Code list for dbsnp_val_status - codelist scheme"@en;
390
+ rdfs:label "Code list for dbsnp_val_status - codelist scheme"@en;
391
+ skos:notation "CL_DBSNP_VAL_STATUS";
392
+ skos:note "Specifies the dbsnp_val_status for each observation";
393
+ skos:hasTopConcept <code/dbsnp_val_status/by1000genomes> ;
394
+ skos:hasTopConcept <code/dbsnp_val_status/by2Hit2Allele> ;
395
+ skos:hasTopConcept <code/dbsnp_val_status/byCluster> ;
396
+ skos:hasTopConcept <code/dbsnp_val_status/byFrequency> ;
397
+ skos:hasTopConcept <code/dbsnp_val_status/byHapMap> ;
398
+ skos:hasTopConcept <code/dbsnp_val_status/byOtherPop> ;
399
+ skos:hasTopConcept <code/dbsnp_val_status/bySubmitter> ;
400
+ skos:hasTopConcept <code/dbsnp_val_status/alternate_allele> ;
401
+ .
402
+
403
+ code:Verification_status a rdfs:Class, owl:Class;
404
+ rdfs:subClassOf skos:Concept ;
405
+ rdfs:label "Code list for verification_status - codelist class"@en;
406
+ rdfs:comment "Specifies the verification_status for each observation";
407
+ rdfs:seeAlso code:verification_status .
408
+
409
+ code:verification_status a skos:ConceptScheme;
410
+ skos:prefLabel "Code list for verification_status - codelist scheme"@en;
411
+ rdfs:label "Code list for verification_status - codelist scheme"@en;
412
+ skos:notation "CL_VERIFICATION_STATUS";
413
+ skos:note "Specifies the verification_status for each observation";
414
+ skos:hasTopConcept <code/verification_status/Verified,> ;
415
+ skos:hasTopConcept <code/verification_status/Unknown> ;
416
+ .
417
+
418
+ code:Validation_status a rdfs:Class, owl:Class;
419
+ rdfs:subClassOf skos:Concept ;
420
+ rdfs:label "Code list for validation_status - codelist class"@en;
421
+ rdfs:comment "Specifies the validation_status for each observation";
422
+ rdfs:seeAlso code:validation_status .
423
+
424
+ code:validation_status a skos:ConceptScheme;
425
+ skos:prefLabel "Code list for validation_status - codelist scheme"@en;
426
+ rdfs:label "Code list for validation_status - codelist scheme"@en;
427
+ skos:notation "CL_VALIDATION_STATUS";
428
+ skos:note "Specifies the validation_status for each observation";
429
+ skos:hasTopConcept <code/validation_status/Untested> ;
430
+ skos:hasTopConcept <code/validation_status/Inconclusive> ;
431
+ skos:hasTopConcept <code/validation_status/Valid> ;
432
+ skos:hasTopConcept <code/validation_status/Invalid> ;
433
+ .
434
+
435
+ code:Mutation_status a rdfs:Class, owl:Class;
436
+ rdfs:subClassOf skos:Concept ;
437
+ rdfs:label "Code list for mutation_status - codelist class"@en;
438
+ rdfs:comment "Specifies the mutation_status for each observation";
439
+ rdfs:seeAlso code:mutation_status .
440
+
441
+ code:mutation_status a skos:ConceptScheme;
442
+ skos:prefLabel "Code list for mutation_status - codelist scheme"@en;
443
+ rdfs:label "Code list for mutation_status - codelist scheme"@en;
444
+ skos:notation "CL_MUTATION_STATUS";
445
+ skos:note "Specifies the mutation_status for each observation";
446
+ skos:hasTopConcept <code/mutation_status/None> ;
447
+ skos:hasTopConcept <code/mutation_status/Germline> ;
448
+ skos:hasTopConcept <code/mutation_status/Somatic> ;
449
+ skos:hasTopConcept <code/mutation_status/LOH> ;
450
+ skos:hasTopConcept <code/mutation_status/Post-transcriptional> ;
451
+ skos:hasTopConcept <code/mutation_status/modification> ;
452
+ skos:hasTopConcept <code/mutation_status/Unknown> ;
453
+ .
454
+
455
+ code:Sequence_source a rdfs:Class, owl:Class;
456
+ rdfs:subClassOf skos:Concept ;
457
+ rdfs:label "Code list for sequence_source - codelist class"@en;
458
+ rdfs:comment "Specifies the sequence_source for each observation";
459
+ rdfs:seeAlso code:sequence_source .
460
+
461
+ code:sequence_source a skos:ConceptScheme;
462
+ skos:prefLabel "Code list for sequence_source - codelist scheme"@en;
463
+ rdfs:label "Code list for sequence_source - codelist scheme"@en;
464
+ skos:notation "CL_SEQUENCE_SOURCE";
465
+ skos:note "Specifies the sequence_source for each observation";
466
+ skos:hasTopConcept <code/sequence_source/WGS> ;
467
+ skos:hasTopConcept <code/sequence_source/WGA> ;
468
+ skos:hasTopConcept <code/sequence_source/WXS> ;
469
+ skos:hasTopConcept <code/sequence_source/RNA-Seq> ;
470
+ skos:hasTopConcept <code/sequence_source/miRNA-Seq> ;
471
+ skos:hasTopConcept <code/sequence_source/Bisulfite-Seq> ;
472
+ skos:hasTopConcept <code/sequence_source/VALIDATION> ;
473
+ skos:hasTopConcept <code/sequence_source/Other> ;
474
+ skos:hasTopConcept <code/sequence_source/ncRNA-Seq> ;
475
+ skos:hasTopConcept <code/sequence_source/WCS> ;
476
+ skos:hasTopConcept <code/sequence_source/CLONE> ;
477
+ skos:hasTopConcept <code/sequence_source/POOLCLONE> ;
478
+ skos:hasTopConcept <code/sequence_source/AMPLICON> ;
479
+ skos:hasTopConcept <code/sequence_source/CLONEEND> ;
480
+ skos:hasTopConcept <code/sequence_source/FINISHING> ;
481
+ skos:hasTopConcept <code/sequence_source/ChIP-Seq> ;
482
+ skos:hasTopConcept <code/sequence_source/MNase-Seq> ;
483
+ skos:hasTopConcept <code/sequence_source/DNase-Hypersensitivity> ;
484
+ skos:hasTopConcept <code/sequence_source/EST> ;
485
+ skos:hasTopConcept <code/sequence_source/FL-cDNA> ;
486
+ skos:hasTopConcept <code/sequence_source/CTS> ;
487
+ skos:hasTopConcept <code/sequence_source/MRE-Seq> ;
488
+ skos:hasTopConcept <code/sequence_source/MeDIP-Seq> ;
489
+ skos:hasTopConcept <code/sequence_source/MBD-Seq> ;
490
+ skos:hasTopConcept <code/sequence_source/Tn-Seq> ;
491
+ skos:hasTopConcept <code/sequence_source/FAIRE-seq> ;
492
+ skos:hasTopConcept <code/sequence_source/SELEX> ;
493
+ skos:hasTopConcept <code/sequence_source/RIP-Seq> ;
494
+ skos:hasTopConcept <code/sequence_source/ChIA-PET> ;
495
+ .
496
+
497
+ code:Sequencer a rdfs:Class, owl:Class;
498
+ rdfs:subClassOf skos:Concept ;
499
+ rdfs:label "Code list for sequencer - codelist class"@en;
500
+ rdfs:comment "Specifies the sequencer for each observation";
501
+ rdfs:seeAlso code:sequencer .
502
+
503
+ code:sequencer a skos:ConceptScheme;
504
+ skos:prefLabel "Code list for sequencer - codelist scheme"@en;
505
+ rdfs:label "Code list for sequencer - codelist scheme"@en;
506
+ skos:notation "CL_SEQUENCER";
507
+ skos:note "Specifies the sequencer for each observation";
508
+ skos:hasTopConcept <code/sequencer/Illumina_GAIIx> ;
509
+ skos:hasTopConcept <code/sequencer/Illumina_HiSeq> ;
510
+ skos:hasTopConcept <code/sequencer/SOLID> ;
511
+ skos:hasTopConcept <code/sequencer/454> ;
512
+ skos:hasTopConcept <code/sequencer/ABI_3730xl> ;
513
+ skos:hasTopConcept <code/sequencer/Ion_Torrent_PGM> ;
514
+ skos:hasTopConcept <code/sequencer/Ion_Torrent_Proton> ;
515
+ skos:hasTopConcept <code/sequencer/PacBio_RS> ;
516
+ skos:hasTopConcept <code/sequencer/Illumina_MiSeq> ;
517
+ skos:hasTopConcept <code/sequencer/Illumina_HiSeq_2500> ;
518
+ skos:hasTopConcept <code/sequencer/454_GS_FLX_Titanium> ;
519
+ skos:hasTopConcept <code/sequencer/AB_SOLiD_4_System> ;
520
+ .
521
+
522
+ <code/variant_classification/Frame_Shift_Del> a skos:Concept, code:Variant_classification;
523
+ skos:topConceptOf code:variant_classification ;
524
+ skos:prefLabel "Frame_Shift_Del" ;
525
+ skos:inScheme code:variant_classification .
526
+
527
+ <code/variant_classification/Frame_Shift_Ins> a skos:Concept, code:Variant_classification;
528
+ skos:topConceptOf code:variant_classification ;
529
+ skos:prefLabel "Frame_Shift_Ins" ;
530
+ skos:inScheme code:variant_classification .
531
+
532
+ <code/variant_classification/In_Frame_Del> a skos:Concept, code:Variant_classification;
533
+ skos:topConceptOf code:variant_classification ;
534
+ skos:prefLabel "In_Frame_Del" ;
535
+ skos:inScheme code:variant_classification .
536
+
537
+ <code/variant_classification/In_Frame_Ins> a skos:Concept, code:Variant_classification;
538
+ skos:topConceptOf code:variant_classification ;
539
+ skos:prefLabel "In_Frame_Ins" ;
540
+ skos:inScheme code:variant_classification .
541
+
542
+ <code/variant_classification/Missense_Mutation> a skos:Concept, code:Variant_classification;
543
+ skos:topConceptOf code:variant_classification ;
544
+ skos:prefLabel "Missense_Mutation" ;
545
+ skos:inScheme code:variant_classification .
546
+
547
+ <code/variant_classification/Nonsense_Mutation> a skos:Concept, code:Variant_classification;
548
+ skos:topConceptOf code:variant_classification ;
549
+ skos:prefLabel "Nonsense_Mutation" ;
550
+ skos:inScheme code:variant_classification .
551
+
552
+ <code/variant_classification/Silent> a skos:Concept, code:Variant_classification;
553
+ skos:topConceptOf code:variant_classification ;
554
+ skos:prefLabel "Silent" ;
555
+ skos:inScheme code:variant_classification .
556
+
557
+ <code/variant_classification/Splice_Site> a skos:Concept, code:Variant_classification;
558
+ skos:topConceptOf code:variant_classification ;
559
+ skos:prefLabel "Splice_Site" ;
560
+ skos:inScheme code:variant_classification .
561
+
562
+ <code/variant_classification/Translation_Start_Site> a skos:Concept, code:Variant_classification;
563
+ skos:topConceptOf code:variant_classification ;
564
+ skos:prefLabel "Translation_Start_Site" ;
565
+ skos:inScheme code:variant_classification .
566
+
567
+ <code/variant_classification/Nonstop_Mutation> a skos:Concept, code:Variant_classification;
568
+ skos:topConceptOf code:variant_classification ;
569
+ skos:prefLabel "Nonstop_Mutation" ;
570
+ skos:inScheme code:variant_classification .
571
+
572
+ <code/variant_classification/3'UTR> a skos:Concept, code:Variant_classification;
573
+ skos:topConceptOf code:variant_classification ;
574
+ skos:prefLabel "3'UTR" ;
575
+ skos:inScheme code:variant_classification .
576
+
577
+ <code/variant_classification/3'Flank> a skos:Concept, code:Variant_classification;
578
+ skos:topConceptOf code:variant_classification ;
579
+ skos:prefLabel "3'Flank" ;
580
+ skos:inScheme code:variant_classification .
581
+
582
+ <code/variant_classification/5'UTR> a skos:Concept, code:Variant_classification;
583
+ skos:topConceptOf code:variant_classification ;
584
+ skos:prefLabel "5'UTR" ;
585
+ skos:inScheme code:variant_classification .
586
+
587
+ <code/variant_classification/5'Flank> a skos:Concept, code:Variant_classification;
588
+ skos:topConceptOf code:variant_classification ;
589
+ skos:prefLabel "5'Flank" ;
590
+ skos:inScheme code:variant_classification .
591
+
592
+ <code/variant_classification/IGR1> a skos:Concept, code:Variant_classification;
593
+ skos:topConceptOf code:variant_classification ;
594
+ skos:prefLabel "IGR1" ;
595
+ skos:inScheme code:variant_classification .
596
+
597
+ <code/variant_classification/Intron> a skos:Concept, code:Variant_classification;
598
+ skos:topConceptOf code:variant_classification ;
599
+ skos:prefLabel "Intron" ;
600
+ skos:inScheme code:variant_classification .
601
+
602
+ <code/variant_classification/RNA> a skos:Concept, code:Variant_classification;
603
+ skos:topConceptOf code:variant_classification ;
604
+ skos:prefLabel "RNA" ;
605
+ skos:inScheme code:variant_classification .
606
+
607
+ <code/variant_classification/Targeted_Region> a skos:Concept, code:Variant_classification;
608
+ skos:topConceptOf code:variant_classification ;
609
+ skos:prefLabel "Targeted_Region" ;
610
+ skos:inScheme code:variant_classification .
611
+
612
+ <code/variant_type/SNP> a skos:Concept, code:Variant_type;
613
+ skos:topConceptOf code:variant_type ;
614
+ skos:prefLabel "SNP" ;
615
+ skos:inScheme code:variant_type .
616
+
617
+ <code/variant_type/DNP> a skos:Concept, code:Variant_type;
618
+ skos:topConceptOf code:variant_type ;
619
+ skos:prefLabel "DNP" ;
620
+ skos:inScheme code:variant_type .
621
+
622
+ <code/variant_type/TNP> a skos:Concept, code:Variant_type;
623
+ skos:topConceptOf code:variant_type ;
624
+ skos:prefLabel "TNP" ;
625
+ skos:inScheme code:variant_type .
626
+
627
+ <code/variant_type/ONP> a skos:Concept, code:Variant_type;
628
+ skos:topConceptOf code:variant_type ;
629
+ skos:prefLabel "ONP" ;
630
+ skos:inScheme code:variant_type .
631
+
632
+ <code/variant_type/INS> a skos:Concept, code:Variant_type;
633
+ skos:topConceptOf code:variant_type ;
634
+ skos:prefLabel "INS" ;
635
+ skos:inScheme code:variant_type .
636
+
637
+ <code/variant_type/DEL> a skos:Concept, code:Variant_type;
638
+ skos:topConceptOf code:variant_type ;
639
+ skos:prefLabel "DEL" ;
640
+ skos:inScheme code:variant_type .
641
+
642
+ <code/variant_type/Consolidated> a skos:Concept, code:Variant_type;
643
+ skos:topConceptOf code:variant_type ;
644
+ skos:prefLabel "Consolidated" ;
645
+ skos:inScheme code:variant_type .
646
+
647
+ <code/dbsnp_val_status/by1000genomes> a skos:Concept, code:Dbsnp_val_status;
648
+ skos:topConceptOf code:dbsnp_val_status ;
649
+ skos:prefLabel "by1000genomes" ;
650
+ skos:inScheme code:dbsnp_val_status .
651
+
652
+ <code/dbsnp_val_status/by2Hit2Allele> a skos:Concept, code:Dbsnp_val_status;
653
+ skos:topConceptOf code:dbsnp_val_status ;
654
+ skos:prefLabel "by2Hit2Allele" ;
655
+ skos:inScheme code:dbsnp_val_status .
656
+
657
+ <code/dbsnp_val_status/byCluster> a skos:Concept, code:Dbsnp_val_status;
658
+ skos:topConceptOf code:dbsnp_val_status ;
659
+ skos:prefLabel "byCluster" ;
660
+ skos:inScheme code:dbsnp_val_status .
661
+
662
+ <code/dbsnp_val_status/byFrequency> a skos:Concept, code:Dbsnp_val_status;
663
+ skos:topConceptOf code:dbsnp_val_status ;
664
+ skos:prefLabel "byFrequency" ;
665
+ skos:inScheme code:dbsnp_val_status .
666
+
667
+ <code/dbsnp_val_status/byHapMap> a skos:Concept, code:Dbsnp_val_status;
668
+ skos:topConceptOf code:dbsnp_val_status ;
669
+ skos:prefLabel "byHapMap" ;
670
+ skos:inScheme code:dbsnp_val_status .
671
+
672
+ <code/dbsnp_val_status/byOtherPop> a skos:Concept, code:Dbsnp_val_status;
673
+ skos:topConceptOf code:dbsnp_val_status ;
674
+ skos:prefLabel "byOtherPop" ;
675
+ skos:inScheme code:dbsnp_val_status .
676
+
677
+ <code/dbsnp_val_status/bySubmitter> a skos:Concept, code:Dbsnp_val_status;
678
+ skos:topConceptOf code:dbsnp_val_status ;
679
+ skos:prefLabel "bySubmitter" ;
680
+ skos:inScheme code:dbsnp_val_status .
681
+
682
+ <code/dbsnp_val_status/alternate_allele> a skos:Concept, code:Dbsnp_val_status;
683
+ skos:topConceptOf code:dbsnp_val_status ;
684
+ skos:prefLabel "alternate_allele" ;
685
+ skos:inScheme code:dbsnp_val_status .
686
+
687
+ <code/verification_status/Verified,> a skos:Concept, code:Verification_status;
688
+ skos:topConceptOf code:verification_status ;
689
+ skos:prefLabel "Verified," ;
690
+ skos:inScheme code:verification_status .
691
+
692
+ <code/verification_status/Unknown> a skos:Concept, code:Verification_status;
693
+ skos:topConceptOf code:verification_status ;
694
+ skos:prefLabel "Unknown" ;
695
+ skos:inScheme code:verification_status .
696
+
697
+ <code/validation_status/Untested> a skos:Concept, code:Validation_status;
698
+ skos:topConceptOf code:validation_status ;
699
+ skos:prefLabel "Untested" ;
700
+ skos:inScheme code:validation_status .
701
+
702
+ <code/validation_status/Inconclusive> a skos:Concept, code:Validation_status;
703
+ skos:topConceptOf code:validation_status ;
704
+ skos:prefLabel "Inconclusive" ;
705
+ skos:inScheme code:validation_status .
706
+
707
+ <code/validation_status/Valid> a skos:Concept, code:Validation_status;
708
+ skos:topConceptOf code:validation_status ;
709
+ skos:prefLabel "Valid" ;
710
+ skos:inScheme code:validation_status .
711
+
712
+ <code/validation_status/Invalid> a skos:Concept, code:Validation_status;
713
+ skos:topConceptOf code:validation_status ;
714
+ skos:prefLabel "Invalid" ;
715
+ skos:inScheme code:validation_status .
716
+
717
+ <code/mutation_status/None> a skos:Concept, code:Mutation_status;
718
+ skos:topConceptOf code:mutation_status ;
719
+ skos:prefLabel "None" ;
720
+ skos:inScheme code:mutation_status .
721
+
722
+ <code/mutation_status/Germline> a skos:Concept, code:Mutation_status;
723
+ skos:topConceptOf code:mutation_status ;
724
+ skos:prefLabel "Germline" ;
725
+ skos:inScheme code:mutation_status .
726
+
727
+ <code/mutation_status/Somatic> a skos:Concept, code:Mutation_status;
728
+ skos:topConceptOf code:mutation_status ;
729
+ skos:prefLabel "Somatic" ;
730
+ skos:inScheme code:mutation_status .
731
+
732
+ <code/mutation_status/LOH> a skos:Concept, code:Mutation_status;
733
+ skos:topConceptOf code:mutation_status ;
734
+ skos:prefLabel "LOH" ;
735
+ skos:inScheme code:mutation_status .
736
+
737
+ <code/mutation_status/Post-transcriptional> a skos:Concept, code:Mutation_status;
738
+ skos:topConceptOf code:mutation_status ;
739
+ skos:prefLabel "Post-transcriptional" ;
740
+ skos:inScheme code:mutation_status .
741
+
742
+ <code/mutation_status/modification> a skos:Concept, code:Mutation_status;
743
+ skos:topConceptOf code:mutation_status ;
744
+ skos:prefLabel "modification" ;
745
+ skos:inScheme code:mutation_status .
746
+
747
+ <code/mutation_status/Unknown> a skos:Concept, code:Mutation_status;
748
+ skos:topConceptOf code:mutation_status ;
749
+ skos:prefLabel "Unknown" ;
750
+ skos:inScheme code:mutation_status .
751
+
752
+ <code/sequence_source/WGS> a skos:Concept, code:Sequence_source;
753
+ skos:topConceptOf code:sequence_source ;
754
+ skos:prefLabel "WGS" ;
755
+ skos:inScheme code:sequence_source .
756
+
757
+ <code/sequence_source/WGA> a skos:Concept, code:Sequence_source;
758
+ skos:topConceptOf code:sequence_source ;
759
+ skos:prefLabel "WGA" ;
760
+ skos:inScheme code:sequence_source .
761
+
762
+ <code/sequence_source/WXS> a skos:Concept, code:Sequence_source;
763
+ skos:topConceptOf code:sequence_source ;
764
+ skos:prefLabel "WXS" ;
765
+ skos:inScheme code:sequence_source .
766
+
767
+ <code/sequence_source/RNA-Seq> a skos:Concept, code:Sequence_source;
768
+ skos:topConceptOf code:sequence_source ;
769
+ skos:prefLabel "RNA-Seq" ;
770
+ skos:inScheme code:sequence_source .
771
+
772
+ <code/sequence_source/miRNA-Seq> a skos:Concept, code:Sequence_source;
773
+ skos:topConceptOf code:sequence_source ;
774
+ skos:prefLabel "miRNA-Seq" ;
775
+ skos:inScheme code:sequence_source .
776
+
777
+ <code/sequence_source/Bisulfite-Seq> a skos:Concept, code:Sequence_source;
778
+ skos:topConceptOf code:sequence_source ;
779
+ skos:prefLabel "Bisulfite-Seq" ;
780
+ skos:inScheme code:sequence_source .
781
+
782
+ <code/sequence_source/VALIDATION> a skos:Concept, code:Sequence_source;
783
+ skos:topConceptOf code:sequence_source ;
784
+ skos:prefLabel "VALIDATION" ;
785
+ skos:inScheme code:sequence_source .
786
+
787
+ <code/sequence_source/Other> a skos:Concept, code:Sequence_source;
788
+ skos:topConceptOf code:sequence_source ;
789
+ skos:prefLabel "Other" ;
790
+ skos:inScheme code:sequence_source .
791
+
792
+ <code/sequence_source/ncRNA-Seq> a skos:Concept, code:Sequence_source;
793
+ skos:topConceptOf code:sequence_source ;
794
+ skos:prefLabel "ncRNA-Seq" ;
795
+ skos:inScheme code:sequence_source .
796
+
797
+ <code/sequence_source/WCS> a skos:Concept, code:Sequence_source;
798
+ skos:topConceptOf code:sequence_source ;
799
+ skos:prefLabel "WCS" ;
800
+ skos:inScheme code:sequence_source .
801
+
802
+ <code/sequence_source/CLONE> a skos:Concept, code:Sequence_source;
803
+ skos:topConceptOf code:sequence_source ;
804
+ skos:prefLabel "CLONE" ;
805
+ skos:inScheme code:sequence_source .
806
+
807
+ <code/sequence_source/POOLCLONE> a skos:Concept, code:Sequence_source;
808
+ skos:topConceptOf code:sequence_source ;
809
+ skos:prefLabel "POOLCLONE" ;
810
+ skos:inScheme code:sequence_source .
811
+
812
+ <code/sequence_source/AMPLICON> a skos:Concept, code:Sequence_source;
813
+ skos:topConceptOf code:sequence_source ;
814
+ skos:prefLabel "AMPLICON" ;
815
+ skos:inScheme code:sequence_source .
816
+
817
+ <code/sequence_source/CLONEEND> a skos:Concept, code:Sequence_source;
818
+ skos:topConceptOf code:sequence_source ;
819
+ skos:prefLabel "CLONEEND" ;
820
+ skos:inScheme code:sequence_source .
821
+
822
+ <code/sequence_source/FINISHING> a skos:Concept, code:Sequence_source;
823
+ skos:topConceptOf code:sequence_source ;
824
+ skos:prefLabel "FINISHING" ;
825
+ skos:inScheme code:sequence_source .
826
+
827
+ <code/sequence_source/ChIP-Seq> a skos:Concept, code:Sequence_source;
828
+ skos:topConceptOf code:sequence_source ;
829
+ skos:prefLabel "ChIP-Seq" ;
830
+ skos:inScheme code:sequence_source .
831
+
832
+ <code/sequence_source/MNase-Seq> a skos:Concept, code:Sequence_source;
833
+ skos:topConceptOf code:sequence_source ;
834
+ skos:prefLabel "MNase-Seq" ;
835
+ skos:inScheme code:sequence_source .
836
+
837
+ <code/sequence_source/DNase-Hypersensitivity> a skos:Concept, code:Sequence_source;
838
+ skos:topConceptOf code:sequence_source ;
839
+ skos:prefLabel "DNase-Hypersensitivity" ;
840
+ skos:inScheme code:sequence_source .
841
+
842
+ <code/sequence_source/EST> a skos:Concept, code:Sequence_source;
843
+ skos:topConceptOf code:sequence_source ;
844
+ skos:prefLabel "EST" ;
845
+ skos:inScheme code:sequence_source .
846
+
847
+ <code/sequence_source/FL-cDNA> a skos:Concept, code:Sequence_source;
848
+ skos:topConceptOf code:sequence_source ;
849
+ skos:prefLabel "FL-cDNA" ;
850
+ skos:inScheme code:sequence_source .
851
+
852
+ <code/sequence_source/CTS> a skos:Concept, code:Sequence_source;
853
+ skos:topConceptOf code:sequence_source ;
854
+ skos:prefLabel "CTS" ;
855
+ skos:inScheme code:sequence_source .
856
+
857
+ <code/sequence_source/MRE-Seq> a skos:Concept, code:Sequence_source;
858
+ skos:topConceptOf code:sequence_source ;
859
+ skos:prefLabel "MRE-Seq" ;
860
+ skos:inScheme code:sequence_source .
861
+
862
+ <code/sequence_source/MeDIP-Seq> a skos:Concept, code:Sequence_source;
863
+ skos:topConceptOf code:sequence_source ;
864
+ skos:prefLabel "MeDIP-Seq" ;
865
+ skos:inScheme code:sequence_source .
866
+
867
+ <code/sequence_source/MBD-Seq> a skos:Concept, code:Sequence_source;
868
+ skos:topConceptOf code:sequence_source ;
869
+ skos:prefLabel "MBD-Seq" ;
870
+ skos:inScheme code:sequence_source .
871
+
872
+ <code/sequence_source/Tn-Seq> a skos:Concept, code:Sequence_source;
873
+ skos:topConceptOf code:sequence_source ;
874
+ skos:prefLabel "Tn-Seq" ;
875
+ skos:inScheme code:sequence_source .
876
+
877
+ <code/sequence_source/FAIRE-seq> a skos:Concept, code:Sequence_source;
878
+ skos:topConceptOf code:sequence_source ;
879
+ skos:prefLabel "FAIRE-seq" ;
880
+ skos:inScheme code:sequence_source .
881
+
882
+ <code/sequence_source/SELEX> a skos:Concept, code:Sequence_source;
883
+ skos:topConceptOf code:sequence_source ;
884
+ skos:prefLabel "SELEX" ;
885
+ skos:inScheme code:sequence_source .
886
+
887
+ <code/sequence_source/RIP-Seq> a skos:Concept, code:Sequence_source;
888
+ skos:topConceptOf code:sequence_source ;
889
+ skos:prefLabel "RIP-Seq" ;
890
+ skos:inScheme code:sequence_source .
891
+
892
+ <code/sequence_source/ChIA-PET> a skos:Concept, code:Sequence_source;
893
+ skos:topConceptOf code:sequence_source ;
894
+ skos:prefLabel "ChIA-PET" ;
895
+ skos:inScheme code:sequence_source .
896
+
897
+ <code/sequencer/Illumina_GAIIx> a skos:Concept, code:Sequencer;
898
+ skos:topConceptOf code:sequencer ;
899
+ skos:prefLabel "Illumina_GAIIx" ;
900
+ skos:inScheme code:sequencer .
901
+
902
+ <code/sequencer/Illumina_HiSeq> a skos:Concept, code:Sequencer;
903
+ skos:topConceptOf code:sequencer ;
904
+ skos:prefLabel "Illumina_HiSeq" ;
905
+ skos:inScheme code:sequencer .
906
+
907
+ <code/sequencer/SOLID> a skos:Concept, code:Sequencer;
908
+ skos:topConceptOf code:sequencer ;
909
+ skos:prefLabel "SOLID" ;
910
+ skos:inScheme code:sequencer .
911
+
912
+ <code/sequencer/454> a skos:Concept, code:Sequencer;
913
+ skos:topConceptOf code:sequencer ;
914
+ skos:prefLabel "454" ;
915
+ skos:inScheme code:sequencer .
916
+
917
+ <code/sequencer/ABI_3730xl> a skos:Concept, code:Sequencer;
918
+ skos:topConceptOf code:sequencer ;
919
+ skos:prefLabel "ABI_3730xl" ;
920
+ skos:inScheme code:sequencer .
921
+
922
+ <code/sequencer/Ion_Torrent_PGM> a skos:Concept, code:Sequencer;
923
+ skos:topConceptOf code:sequencer ;
924
+ skos:prefLabel "Ion_Torrent_PGM" ;
925
+ skos:inScheme code:sequencer .
926
+
927
+ <code/sequencer/Ion_Torrent_Proton> a skos:Concept, code:Sequencer;
928
+ skos:topConceptOf code:sequencer ;
929
+ skos:prefLabel "Ion_Torrent_Proton" ;
930
+ skos:inScheme code:sequencer .
931
+
932
+ <code/sequencer/PacBio_RS> a skos:Concept, code:Sequencer;
933
+ skos:topConceptOf code:sequencer ;
934
+ skos:prefLabel "PacBio_RS" ;
935
+ skos:inScheme code:sequencer .
936
+
937
+ <code/sequencer/Illumina_MiSeq> a skos:Concept, code:Sequencer;
938
+ skos:topConceptOf code:sequencer ;
939
+ skos:prefLabel "Illumina_MiSeq" ;
940
+ skos:inScheme code:sequencer .
941
+
942
+ <code/sequencer/Illumina_HiSeq_2500> a skos:Concept, code:Sequencer;
943
+ skos:topConceptOf code:sequencer ;
944
+ skos:prefLabel "Illumina_HiSeq_2500" ;
945
+ skos:inScheme code:sequencer .
946
+
947
+ <code/sequencer/454_GS_FLX_Titanium> a skos:Concept, code:Sequencer;
948
+ skos:topConceptOf code:sequencer ;
949
+ skos:prefLabel "454_GS_FLX_Titanium" ;
950
+ skos:inScheme code:sequencer .
951
+
952
+ <code/sequencer/AB_SOLiD_4_System> a skos:Concept, code:Sequencer;
953
+ skos:topConceptOf code:sequencer ;
954
+ skos:prefLabel "AB_SOLiD_4_System" ;
955
+ skos:inScheme code:sequencer .
956
+
957
+ ns:obs2 a qb:Observation ;
958
+ qb:dataSet ns:dataset-maf_example ;
959
+ prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
960
+ prop:Variant_Type <code/variant_type/SNP> ;
961
+ prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
962
+ prop:Verification_Status <code/verification_status/Unknown> ;
963
+ prop:Validation_Status <code/validation_status/Untested> ;
964
+ prop:Mutation_Status <code/mutation_status/Somatic> ;
965
+ prop:Sequence_Source <code/sequence_source/WXS> ;
966
+ prop:Sequencer <code/sequencer/Illumina_GAIIx> ;
967
+ prop:Hugo_Symbol <http://identifiers.org/hgnc.symbol/A1BG> ;
968
+ prop:Center "genome.wustl.edu" ;
969
+ prop:NCBI_Build 37 ;
970
+ prop:Chromosome 19 ;
971
+ prop:Start_Position 58862784 ;
972
+ prop:End_Position 58862784 ;
973
+ prop:Strand "+" ;
974
+ prop:Reference_Allele "C" ;
975
+ prop:Tumor_Seq_Allele1 "C" ;
976
+ prop:Tumor_Seq_Allele2 "T" ;
977
+ prop:dbSNP_RS "novel" ;
978
+ prop:Tumor_Sample_Barcode "TCGA-E9-A22B-01A-11D-A159-09" ;
979
+ prop:Matched_Norm_Sample_Barcode "TCGA-E9-A22B-10A-01D-A159-09" ;
980
+ prop:Match_Norm_Seq_Allele1 "C" ;
981
+ prop:Match_Norm_Seq_Allele2 "C" ;
982
+ prop:Sequencing_Phase "Phase_IV" ;
983
+ prop:Validation_Method "none" ;
984
+ prop:Score 1 ;
985
+ prop:BAM_File "dbGAP" ;
986
+ prop:Tumor_Sample_UUID "e46a5d19-2dd7-4c34-8fff-6276278c58b3" ;
987
+ prop:Matched_Norm_Sample_UUID "f948182a-f814-4e3c-83ee-82b78aa423c1" ;
988
+ prop:patient_id "E9-A22B" ;
989
+ prop:sample_id "01A-11D-A159-09" ;
990
+ .
991
+
992
+ ns:obs3 a qb:Observation ;
993
+ qb:dataSet ns:dataset-maf_example ;
994
+ prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
995
+ prop:Variant_Type <code/variant_type/SNP> ;
996
+ prop:dbSNP_Val_Status <code/dbsnp_val_status/byFrequency> ;
997
+ prop:Verification_Status <code/verification_status/Unknown> ;
998
+ prop:Validation_Status <code/validation_status/Untested> ;
999
+ prop:Mutation_Status <code/mutation_status/Somatic> ;
1000
+ prop:Sequence_Source <code/sequence_source/WXS> ;
1001
+ prop:Sequencer <code/sequencer/Illumina_GAIIx> ;
1002
+ prop:Hugo_Symbol <http://identifiers.org/hgnc.symbol/A1BG> ;
1003
+ prop:Center "genome.wustl.edu" ;
1004
+ prop:NCBI_Build 37 ;
1005
+ prop:Chromosome 19 ;
1006
+ prop:Start_Position 58864366 ;
1007
+ prop:End_Position 58864366 ;
1008
+ prop:Strand "+" ;
1009
+ prop:Reference_Allele "G" ;
1010
+ prop:Tumor_Seq_Allele1 "G" ;
1011
+ prop:Tumor_Seq_Allele2 "A" ;
1012
+ prop:dbSNP_RS <http://identifiers.org/dbsnp/151098196> ;
1013
+ prop:Tumor_Sample_Barcode "TCGA-E9-A1NH-01A-11D-A14G-09" ;
1014
+ prop:Matched_Norm_Sample_Barcode "TCGA-E9-A1NH-11A-33D-A14G-09" ;
1015
+ prop:Match_Norm_Seq_Allele1 "G" ;
1016
+ prop:Match_Norm_Seq_Allele2 "G" ;
1017
+ prop:Sequencing_Phase "Phase_IV" ;
1018
+ prop:Validation_Method "none" ;
1019
+ prop:Score 1 ;
1020
+ prop:BAM_File "dbGAP" ;
1021
+ prop:Tumor_Sample_UUID "13c312ec-0add-4758-ab8d-c193e2e08c6d" ;
1022
+ prop:Matched_Norm_Sample_UUID "0ee95056-a7cc-415c-a487-3ad08604dfc0" ;
1023
+ prop:patient_id "E9-A1NH" ;
1024
+ prop:sample_id "01A-11D-A14G-09" ;
1025
+ .
1026
+
1027
+ ns:obs4 a qb:Observation ;
1028
+ qb:dataSet ns:dataset-maf_example ;
1029
+ prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
1030
+ prop:Variant_Type <code/variant_type/SNP> ;
1031
+ prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
1032
+ prop:Verification_Status <code/verification_status/Unknown> ;
1033
+ prop:Validation_Status <code/validation_status/Untested> ;
1034
+ prop:Mutation_Status <code/mutation_status/Somatic> ;
1035
+ prop:Sequence_Source <code/sequence_source/WXS> ;
1036
+ prop:Sequencer <code/sequencer/Illumina_GAIIx> ;
1037
+ prop:Hugo_Symbol <http://identifiers.org/hgnc.symbol/A1CF> ;
1038
+ prop:Entrez_Gene_Id <http://identifiers.org/ncbigene/29974> ;
1039
+ prop:Center "genome.wustl.edu" ;
1040
+ prop:NCBI_Build 37 ;
1041
+ prop:Chromosome 10 ;
1042
+ prop:Start_Position 52595854 ;
1043
+ prop:End_Position 52595854 ;
1044
+ prop:Strand "+" ;
1045
+ prop:Reference_Allele "G" ;
1046
+ prop:Tumor_Seq_Allele1 "G" ;
1047
+ prop:Tumor_Seq_Allele2 "A" ;
1048
+ prop:dbSNP_RS "novel" ;
1049
+ prop:Tumor_Sample_Barcode "TCGA-BH-A0HP-01A-12D-A099-09" ;
1050
+ prop:Matched_Norm_Sample_Barcode "TCGA-BH-A0HP-10A-01D-A099-09" ;
1051
+ prop:Match_Norm_Seq_Allele1 "G" ;
1052
+ prop:Match_Norm_Seq_Allele2 "G" ;
1053
+ prop:Sequencing_Phase "Phase_IV" ;
1054
+ prop:Validation_Method "none" ;
1055
+ prop:Score 1 ;
1056
+ prop:BAM_File "dbGAP" ;
1057
+ prop:Tumor_Sample_UUID "ad52a8fb-7a76-4aa0-95fb-d6edab0fe2b2" ;
1058
+ prop:Matched_Norm_Sample_UUID "8c059d33-23de-439a-914a-290527c5efbe" ;
1059
+ prop:patient_id "BH-A0HP" ;
1060
+ prop:sample_id "01A-12D-A099-09" ;
1061
+ .
1062
+
1063
+ ns:obs5 a qb:Observation ;
1064
+ qb:dataSet ns:dataset-maf_example ;
1065
+ prop:Variant_Classification <code/variant_classification/Silent> ;
1066
+ prop:Variant_Type <code/variant_type/SNP> ;
1067
+ prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
1068
+ prop:Verification_Status <code/verification_status/Unknown> ;
1069
+ prop:Validation_Status <code/validation_status/Untested> ;
1070
+ prop:Mutation_Status <code/mutation_status/Somatic> ;
1071
+ prop:Sequence_Source <code/sequence_source/WXS> ;
1072
+ prop:Sequencer <code/sequencer/Illumina_GAIIx> ;
1073
+ prop:Hugo_Symbol <http://identifiers.org/hgnc.symbol/A1CF> ;
1074
+ prop:Entrez_Gene_Id <http://identifiers.org/ncbigene/29974> ;
1075
+ prop:Center "genome.wustl.edu" ;
1076
+ prop:NCBI_Build 37 ;
1077
+ prop:Chromosome 10 ;
1078
+ prop:Start_Position 52595937 ;
1079
+ prop:End_Position 52595937 ;
1080
+ prop:Strand "+" ;
1081
+ prop:Reference_Allele "G" ;
1082
+ prop:Tumor_Seq_Allele1 "G" ;
1083
+ prop:Tumor_Seq_Allele2 "A" ;
1084
+ prop:dbSNP_RS "novel" ;
1085
+ prop:Tumor_Sample_Barcode "TCGA-BH-A18P-01A-11D-A12B-09" ;
1086
+ prop:Matched_Norm_Sample_Barcode "TCGA-BH-A18P-11A-43D-A12B-09" ;
1087
+ prop:Match_Norm_Seq_Allele1 "G" ;
1088
+ prop:Match_Norm_Seq_Allele2 "G" ;
1089
+ prop:Sequencing_Phase "Phase_IV" ;
1090
+ prop:Validation_Method "none" ;
1091
+ prop:Score 1 ;
1092
+ prop:BAM_File "dbGAP" ;
1093
+ prop:Tumor_Sample_UUID "add624a3-57e9-46be-9bcc-3e53d7c2dfb7" ;
1094
+ prop:Matched_Norm_Sample_UUID "5cae8dca-b28a-4483-9c03-6f0645161c04" ;
1095
+ prop:patient_id "BH-A18P" ;
1096
+ prop:sample_id "01A-11D-A12B-09" ;
1097
+ .
1098
+
1099
+ ns:obs6 a qb:Observation ;
1100
+ qb:dataSet ns:dataset-maf_example ;
1101
+ prop:Variant_Classification <code/variant_classification/Silent> ;
1102
+ prop:Variant_Type <code/variant_type/SNP> ;
1103
+ prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
1104
+ prop:Verification_Status <code/verification_status/Unknown> ;
1105
+ prop:Validation_Status <code/validation_status/Untested> ;
1106
+ prop:Mutation_Status <code/mutation_status/Somatic> ;
1107
+ prop:Sequence_Source <code/sequence_source/WXS> ;
1108
+ prop:Sequencer <code/sequencer/Illumina_GAIIx> ;
1109
+ prop:Hugo_Symbol <http://identifiers.org/hgnc.symbol/A2BP1> ;
1110
+ prop:Center "genome.wustl.edu" ;
1111
+ prop:NCBI_Build 37 ;
1112
+ prop:Chromosome 16 ;
1113
+ prop:Start_Position 7568361 ;
1114
+ prop:End_Position 7568361 ;
1115
+ prop:Strand "+" ;
1116
+ prop:Reference_Allele "G" ;
1117
+ prop:Tumor_Seq_Allele1 "G" ;
1118
+ prop:Tumor_Seq_Allele2 "C" ;
1119
+ prop:dbSNP_RS "novel" ;
1120
+ prop:Tumor_Sample_Barcode "TCGA-D8-A1JN-01A-11D-A13L-09" ;
1121
+ prop:Matched_Norm_Sample_Barcode "TCGA-D8-A1JN-10A-01D-A13O-09" ;
1122
+ prop:Match_Norm_Seq_Allele1 "G" ;
1123
+ prop:Match_Norm_Seq_Allele2 "G" ;
1124
+ prop:Sequencing_Phase "Phase_IV" ;
1125
+ prop:Validation_Method "none" ;
1126
+ prop:Score 1 ;
1127
+ prop:BAM_File "dbGAP" ;
1128
+ prop:Tumor_Sample_UUID "c83c7d48-8671-4f27-b3dd-05411fa2f784" ;
1129
+ prop:Matched_Norm_Sample_UUID "c14cac2a-e308-44fa-b1af-ee51511ee0ee" ;
1130
+ prop:patient_id "D8-A1JN" ;
1131
+ prop:sample_id "01A-11D-A13L-09" ;
1132
+ .
1133
+
1134
+ ns:obs7 a qb:Observation ;
1135
+ qb:dataSet ns:dataset-maf_example ;
1136
+ prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
1137
+ prop:Variant_Type <code/variant_type/SNP> ;
1138
+ prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
1139
+ prop:Verification_Status <code/verification_status/Unknown> ;
1140
+ prop:Validation_Status <code/validation_status/Valid> ;
1141
+ prop:Mutation_Status <code/mutation_status/Somatic> ;
1142
+ prop:Sequence_Source <code/sequence_source/WXS> ;
1143
+ prop:Sequencer <code/sequencer/Illumina_GAIIx> ;
1144
+ prop:Hugo_Symbol <http://identifiers.org/hgnc.symbol/A2BP1> ;
1145
+ prop:Entrez_Gene_Id <http://identifiers.org/ncbigene/54715> ;
1146
+ prop:Center "genome.wustl.edu" ;
1147
+ prop:NCBI_Build 37 ;
1148
+ prop:Chromosome 16 ;
1149
+ prop:Start_Position 7102099 ;
1150
+ prop:End_Position 7102099 ;
1151
+ prop:Strand "+" ;
1152
+ prop:Reference_Allele "G" ;
1153
+ prop:Tumor_Seq_Allele1 "G" ;
1154
+ prop:Tumor_Seq_Allele2 "T" ;
1155
+ prop:dbSNP_RS "novel" ;
1156
+ prop:Tumor_Sample_Barcode "TCGA-E2-A1BC-01A-11D-A14G-09" ;
1157
+ prop:Matched_Norm_Sample_Barcode "TCGA-E2-A1BC-10A-01D-A12Q-09" ;
1158
+ prop:Match_Norm_Seq_Allele1 "G" ;
1159
+ prop:Match_Norm_Seq_Allele2 "G" ;
1160
+ prop:Tumor_Validation_Allele1 "G" ;
1161
+ prop:Tumor_Validation_Allele2 "T" ;
1162
+ prop:Match_Norm_Validation_Allele1 "G" ;
1163
+ prop:Match_Norm_Validation_Allele2 "G" ;
1164
+ prop:Sequencing_Phase "Phase_IV" ;
1165
+ prop:Validation_Method "Illumina_WXS_gDNA" ;
1166
+ prop:Score 1 ;
1167
+ prop:BAM_File "dbGAP" ;
1168
+ prop:Tumor_Sample_UUID "5947a9db-7d13-44ff-86ad-eb5e6c8dcec5" ;
1169
+ prop:Matched_Norm_Sample_UUID "6a4cd52f-2247-4caf-9b37-e90b02fd4d8b" ;
1170
+ prop:patient_id "E2-A1BC" ;
1171
+ prop:sample_id "01A-11D-A14G-09" ;
1172
+ .
1173
+