table.sql 30.4 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13
CREATE TABLE `allele` (
  `allele_id` int(11) NOT NULL AUTO_INCREMENT,
  `variation_id` int(11) unsigned NOT NULL,
  `subsnp_id` int(11) unsigned DEFAULT NULL,
  `allele_code_id` int(11) unsigned NOT NULL,
  `population_id` int(11) unsigned DEFAULT NULL,
  `frequency` float unsigned DEFAULT NULL,
  `count` int(11) unsigned DEFAULT NULL,
  `frequency_submitter_handle` int(10) DEFAULT NULL,
  PRIMARY KEY (`allele_id`),
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`),
  KEY `population_idx` (`population_id`)
14
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
15 16 17

CREATE TABLE `allele_code` (
  `allele_code_id` int(11) NOT NULL AUTO_INCREMENT,
18
  `allele` varchar(60000) DEFAULT NULL,
19
  PRIMARY KEY (`allele_code_id`),
20
  UNIQUE KEY `allele_idx` (`allele`(1000))
Anja Thormann's avatar
Anja Thormann committed
21
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
22

23 24 25 26 27 28 29 30 31 32
CREATE TABLE `allele_synonym` (
  `allele_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `variation_id` int(10) unsigned NOT NULL,
  `hgvs_genomic` varchar(600) NOT NULL,
  `name` varchar(255) NOT NULL,
  PRIMARY KEY (`allele_synonym_id`),
  UNIQUE KEY `variation_name_idx` (`variation_id`,`name`),
  KEY `name_idx` (`name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

33 34 35 36
CREATE TABLE `associate_study` (
  `study1_id` int(10) unsigned NOT NULL,
  `study2_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`study1_id`,`study2_id`)
Anja Thormann's avatar
Anja Thormann committed
37
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
38

39
CREATE TABLE `attrib` (
Magali Ruffier's avatar
Magali Ruffier committed
40
  `attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
41 42 43 44
  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
  `value` text NOT NULL,
  PRIMARY KEY (`attrib_id`),
  UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
45
) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;
46

47 48 49 50 51
CREATE TABLE `attrib_set` (
  `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
  `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
  UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
  KEY `attrib_idx` (`attrib_id`)
Anja Thormann's avatar
Anja Thormann committed
52
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
53

54 55 56 57 58 59 60
CREATE TABLE `attrib_type` (
  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
  `code` varchar(20) NOT NULL DEFAULT '',
  `name` varchar(255) NOT NULL DEFAULT '',
  `description` text,
  PRIMARY KEY (`attrib_type_id`),
  UNIQUE KEY `code_idx` (`code`)
Anja Thormann's avatar
Anja Thormann committed
61
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
62

63 64 65 66 67 68 69 70 71
CREATE TABLE `compressed_genotype_region` (
  `sample_id` int(10) unsigned NOT NULL,
  `seq_region_id` int(10) unsigned NOT NULL,
  `seq_region_start` int(11) NOT NULL,
  `seq_region_end` int(11) NOT NULL,
  `seq_region_strand` tinyint(4) NOT NULL,
  `genotypes` blob,
  KEY `pos_idx` (`seq_region_id`,`seq_region_start`),
  KEY `sample_idx` (`sample_id`)
Anja Thormann's avatar
Anja Thormann committed
72
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
73

74 75 76 77 78 79
CREATE TABLE `compressed_genotype_var` (
  `variation_id` int(11) unsigned NOT NULL,
  `subsnp_id` int(11) unsigned DEFAULT NULL,
  `genotypes` blob,
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`)
Anja Thormann's avatar
Anja Thormann committed
80
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
81

82 83 84 85 86 87 88 89 90 91 92
CREATE TABLE `coord_system` (
  `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `species_id` int(10) unsigned NOT NULL DEFAULT '1',
  `name` varchar(40) NOT NULL,
  `version` varchar(255) DEFAULT NULL,
  `rank` int(11) NOT NULL,
  `attrib` set('default_version','sequence_level') DEFAULT NULL,
  PRIMARY KEY (`coord_system_id`),
  UNIQUE KEY `rank_idx` (`rank`,`species_id`),
  UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
  KEY `species_idx` (`species_id`)
Anja Thormann's avatar
Anja Thormann committed
93
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
94

95 96 97 98 99 100 101
CREATE TABLE `display_group` (
  `display_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `display_priority` int(10) unsigned NOT NULL,
  `display_name` varchar(255) NOT NULL,
  PRIMARY KEY (`display_group_id`),
  UNIQUE KEY `display_name` (`display_name`),
  UNIQUE KEY `display_priority` (`display_priority`)
Anja Thormann's avatar
Anja Thormann committed
102
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
103

104 105 106 107 108 109
CREATE TABLE `failed_allele` (
  `failed_allele_id` int(11) NOT NULL AUTO_INCREMENT,
  `allele_id` int(10) unsigned NOT NULL,
  `failed_description_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`failed_allele_id`),
  UNIQUE KEY `allele_idx` (`allele_id`,`failed_description_id`)
Anja Thormann's avatar
Anja Thormann committed
110
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
111

112 113 114 115
CREATE TABLE `failed_description` (
  `failed_description_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `description` text NOT NULL,
  PRIMARY KEY (`failed_description_id`)
Anja Thormann's avatar
Anja Thormann committed
116
) ENGINE=MyISAM AUTO_INCREMENT=21 DEFAULT CHARSET=latin1;
117

118 119 120 121 122 123
CREATE TABLE `failed_structural_variation` (
  `failed_structural_variation_id` int(11) NOT NULL AUTO_INCREMENT,
  `structural_variation_id` int(10) unsigned NOT NULL,
  `failed_description_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`failed_structural_variation_id`),
  UNIQUE KEY `structural_variation_idx` (`structural_variation_id`,`failed_description_id`)
Anja Thormann's avatar
Anja Thormann committed
124
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
125

126 127 128 129 130 131
CREATE TABLE `failed_variation` (
  `failed_variation_id` int(11) NOT NULL AUTO_INCREMENT,
  `variation_id` int(10) unsigned NOT NULL,
  `failed_description_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`failed_variation_id`),
  UNIQUE KEY `variation_idx` (`variation_id`,`failed_description_id`)
Anja Thormann's avatar
Anja Thormann committed
132
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
133

134 135 136 137 138 139 140
CREATE TABLE `genotype_code` (
  `genotype_code_id` int(11) unsigned NOT NULL,
  `allele_code_id` int(11) unsigned NOT NULL,
  `haplotype_id` tinyint(2) unsigned NOT NULL,
  `phased` tinyint(2) unsigned DEFAULT NULL,
  KEY `genotype_code_id` (`genotype_code_id`),
  KEY `allele_code_id` (`allele_code_id`)
Anja Thormann's avatar
Anja Thormann committed
141
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
142

143 144 145 146 147 148 149 150 151 152 153
CREATE TABLE `individual` (
  `individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `description` text,
  `gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown',
  `father_individual_id` int(10) unsigned DEFAULT NULL,
  `mother_individual_id` int(10) unsigned DEFAULT NULL,
  `individual_type_id` int(10) unsigned NOT NULL DEFAULT '0',
  PRIMARY KEY (`individual_id`),
  KEY `father_individual_idx` (`father_individual_id`),
  KEY `mother_individual_idx` (`mother_individual_id`)
Anja Thormann's avatar
Anja Thormann committed
154
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
155

156 157 158 159 160 161 162 163
CREATE TABLE `individual_synonym` (
  `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `individual_id` int(10) unsigned NOT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`synonym_id`),
  KEY `individual_idx` (`individual_id`),
  KEY `name` (`name`,`source_id`)
Anja Thormann's avatar
Anja Thormann committed
164
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
165

166 167 168 169 170
CREATE TABLE `individual_type` (
  `individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) NOT NULL,
  `description` text,
  PRIMARY KEY (`individual_type_id`)
Magali Ruffier's avatar
Magali Ruffier committed
171
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
172

173 174 175 176 177 178 179 180
CREATE TABLE `meta` (
  `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `species_id` int(10) unsigned DEFAULT '1',
  `meta_key` varchar(40) NOT NULL,
  `meta_value` varchar(255) NOT NULL,
  PRIMARY KEY (`meta_id`),
  UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
  KEY `species_value_idx` (`species_id`,`meta_value`)
181
) ENGINE=MyISAM AUTO_INCREMENT=38 DEFAULT CHARSET=latin1;
182

183 184 185 186 187
CREATE TABLE `meta_coord` (
  `table_name` varchar(40) NOT NULL,
  `coord_system_id` int(10) unsigned NOT NULL,
  `max_length` int(11) DEFAULT NULL,
  UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
Anja Thormann's avatar
Anja Thormann committed
188
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
189 190 191 192 193 194 195 196

CREATE TABLE `motif_feature_variation` (
  `motif_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `variation_feature_id` int(11) unsigned NOT NULL,
  `feature_stable_id` varchar(128) DEFAULT NULL,
  `motif_feature_id` int(11) unsigned NOT NULL,
  `allele_string` text,
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
197 198
  `consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
  `motif_name` varchar(60) DEFAULT NULL,
199 200 201 202 203 204 205
  `motif_start` int(11) unsigned DEFAULT NULL,
  `motif_end` int(11) unsigned DEFAULT NULL,
  `motif_score_delta` float DEFAULT NULL,
  `in_informative_position` tinyint(1) NOT NULL DEFAULT '0',
  PRIMARY KEY (`motif_feature_variation_id`),
  KEY `variation_feature_idx` (`variation_feature_id`),
  KEY `consequence_type_idx` (`consequence_types`),
206 207
  KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`),
  KEY `feature_stable_idx` (`feature_stable_id`)
Anja Thormann's avatar
Anja Thormann committed
208
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
209

210 211 212 213 214 215 216
CREATE TABLE `phenotype` (
  `phenotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `stable_id` varchar(255) DEFAULT NULL,
  `name` varchar(50) DEFAULT NULL,
  `description` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`phenotype_id`),
  UNIQUE KEY `desc_idx` (`description`),
217 218
  KEY `name_idx` (`name`),
  KEY `stable_idx` (`stable_id`)
219
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
220

221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238
CREATE TABLE `phenotype_feature` (
  `phenotype_feature_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `phenotype_id` int(11) unsigned DEFAULT NULL,
  `source_id` int(11) unsigned DEFAULT NULL,
  `study_id` int(11) unsigned DEFAULT NULL,
  `type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') DEFAULT NULL,
  `object_id` varchar(255) DEFAULT NULL,
  `is_significant` tinyint(1) unsigned DEFAULT '1',
  `seq_region_id` int(11) unsigned DEFAULT NULL,
  `seq_region_start` int(11) unsigned DEFAULT NULL,
  `seq_region_end` int(11) unsigned DEFAULT NULL,
  `seq_region_strand` tinyint(4) DEFAULT NULL,
  PRIMARY KEY (`phenotype_feature_id`),
  KEY `phenotype_idx` (`phenotype_id`),
  KEY `object_idx` (`object_id`,`type`),
  KEY `type_idx` (`type`),
  KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
  KEY `source_idx` (`source_id`)
239
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
240

241 242 243 244 245 246
CREATE TABLE `phenotype_feature_attrib` (
  `phenotype_feature_id` int(11) unsigned NOT NULL,
  `attrib_type_id` int(11) DEFAULT NULL,
  `value` varchar(255) DEFAULT NULL,
  KEY `phenotype_feature_idx` (`phenotype_feature_id`),
  KEY `type_value_idx` (`attrib_type_id`,`value`)
Anja Thormann's avatar
Anja Thormann committed
247
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
248

Alessandro Vullo's avatar
Alessandro Vullo committed
249 250 251
CREATE TABLE `phenotype_ontology_accession` (
  `phenotype_id` int(11) unsigned NOT NULL,
  `accession` varchar(255) NOT NULL,
252
  `mapped_by_attrib` set('437','438','439','440','441','442','443','444','588','589','590','591','592','593','594') DEFAULT NULL,
253 254 255
  `mapping_type` enum('is','involves') DEFAULT NULL,
  PRIMARY KEY (`phenotype_id`,`accession`),
  KEY `accession_idx` (`accession`)
Alessandro Vullo's avatar
Alessandro Vullo committed
256
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
257

258 259 260 261 262 263 264 265 266 267 268
CREATE TABLE `population` (
  `population_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `size` int(10) DEFAULT NULL,
  `description` text,
  `collection` tinyint(1) DEFAULT '0',
  `freqs_from_gts` tinyint(1) DEFAULT NULL,
  `display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
  `display_group_id` tinyint(1) DEFAULT NULL,
  PRIMARY KEY (`population_id`),
  KEY `name_idx` (`name`)
269
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
270

271 272 273 274 275 276 277 278 279 280 281 282
CREATE TABLE `population_genotype` (
  `population_genotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `variation_id` int(11) unsigned NOT NULL,
  `subsnp_id` int(11) unsigned DEFAULT NULL,
  `genotype_code_id` int(11) DEFAULT NULL,
  `frequency` float DEFAULT NULL,
  `population_id` int(10) unsigned DEFAULT NULL,
  `count` int(10) unsigned DEFAULT NULL,
  PRIMARY KEY (`population_genotype_id`),
  KEY `population_idx` (`population_id`),
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`)
Anja Thormann's avatar
Anja Thormann committed
283
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
284

285 286 287 288 289
CREATE TABLE `population_structure` (
  `super_population_id` int(10) unsigned NOT NULL,
  `sub_population_id` int(10) unsigned NOT NULL,
  UNIQUE KEY `super_population_idx` (`super_population_id`,`sub_population_id`),
  KEY `sub_population_idx` (`sub_population_id`)
Anja Thormann's avatar
Anja Thormann committed
290
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
291 292 293 294 295 296 297 298 299

CREATE TABLE `population_synonym` (
  `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `population_id` int(10) unsigned NOT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`synonym_id`),
  KEY `population_idx` (`population_id`),
  KEY `name` (`name`,`source_id`)
Anja Thormann's avatar
Anja Thormann committed
300
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
301 302 303 304 305 306

CREATE TABLE `protein_function_predictions` (
  `translation_md5_id` int(11) unsigned NOT NULL,
  `analysis_attrib_id` int(11) unsigned NOT NULL,
  `prediction_matrix` mediumblob,
  PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`)
Anja Thormann's avatar
Anja Thormann committed
307
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
308

309 310 311 312 313 314
CREATE TABLE `protein_function_predictions_attrib` (
  `translation_md5_id` int(11) unsigned NOT NULL,
  `analysis_attrib_id` int(11) unsigned NOT NULL,
  `attrib_type_id` int(11) unsigned NOT NULL,
  `position_values` blob,
  PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`)
Anja Thormann's avatar
Anja Thormann committed
315
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
316

317 318 319
CREATE TABLE `publication` (
  `publication_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `title` varchar(255) DEFAULT NULL,
320
  `authors` varchar(255) CHARACTER SET latin2 DEFAULT NULL,
321 322 323 324 325 326 327 328
  `pmid` int(10) DEFAULT NULL,
  `pmcid` varchar(255) DEFAULT NULL,
  `year` int(10) unsigned DEFAULT NULL,
  `doi` varchar(50) DEFAULT NULL,
  `ucsc_id` varchar(50) DEFAULT NULL,
  PRIMARY KEY (`publication_id`),
  KEY `pmid_idx` (`pmid`),
  KEY `doi_idx` (`doi`)
Anja Thormann's avatar
Anja Thormann committed
329
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
330

331 332 333 334 335 336
CREATE TABLE `read_coverage` (
  `seq_region_id` int(10) unsigned NOT NULL,
  `seq_region_start` int(11) NOT NULL,
  `seq_region_end` int(11) NOT NULL,
  `level` tinyint(4) NOT NULL,
  `sample_id` int(10) unsigned NOT NULL,
337 338
  KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
  KEY `sample_idx` (`sample_id`)
Anja Thormann's avatar
Anja Thormann committed
339
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
340

341 342 343 344 345 346 347
CREATE TABLE `regulatory_feature_variation` (
  `regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `variation_feature_id` int(11) unsigned NOT NULL,
  `feature_stable_id` varchar(128) DEFAULT NULL,
  `feature_type` text,
  `allele_string` text,
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
348
  `consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL,
349 350 351
  PRIMARY KEY (`regulatory_feature_variation_id`),
  KEY `variation_feature_idx` (`variation_feature_id`),
  KEY `consequence_type_idx` (`consequence_types`),
352 353
  KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`),
  KEY `feature_stable_idx` (`feature_stable_id`)
Anja Thormann's avatar
Anja Thormann committed
354
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
355 356 357 358 359 360 361 362 363 364 365

CREATE TABLE `sample` (
  `sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `individual_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  `description` text,
  `study_id` int(10) unsigned DEFAULT NULL,
  `display` enum('REFERENCE','DEFAULT','DISPLAYABLE','UNDISPLAYABLE','LD','MARTDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
  `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT '0',
  `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') DEFAULT NULL,
  PRIMARY KEY (`sample_id`),
366 367
  KEY `individual_idx` (`individual_id`),
  KEY `study_idx` (`study_id`)
Anja Thormann's avatar
Anja Thormann committed
368
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
369

370 371 372
CREATE TABLE `sample_genotype_multiple_bp` (
  `variation_id` int(10) unsigned NOT NULL,
  `subsnp_id` int(15) unsigned DEFAULT NULL,
373 374
  `allele_1` varchar(25000) DEFAULT NULL,
  `allele_2` varchar(25000) DEFAULT NULL,
375 376 377 378
  `sample_id` int(10) unsigned DEFAULT NULL,
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`),
  KEY `sample_idx` (`sample_id`)
Anja Thormann's avatar
Anja Thormann committed
379
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
380 381 382 383

CREATE TABLE `sample_population` (
  `sample_id` int(10) unsigned NOT NULL,
  `population_id` int(10) unsigned NOT NULL,
384 385
  KEY `sample_idx` (`sample_id`),
  KEY `population_idx` (`population_id`)
Anja Thormann's avatar
Anja Thormann committed
386
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
387

Magali Ruffier's avatar
Magali Ruffier committed
388 389 390 391 392 393 394 395 396
CREATE TABLE `sample_synonym` (
  `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `sample_id` int(10) unsigned NOT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`synonym_id`),
  KEY `sample_idx` (`sample_id`),
  KEY `name` (`name`,`source_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
397

398 399
CREATE TABLE `seq_region` (
  `seq_region_id` int(10) unsigned NOT NULL,
400
  `name` varchar(255) NOT NULL,
401 402 403 404
  `coord_system_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`seq_region_id`),
  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
  KEY `cs_idx` (`coord_system_id`)
Anja Thormann's avatar
Anja Thormann committed
405
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
406

407 408 409 410
CREATE TABLE `source` (
  `source_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(24) NOT NULL,
  `version` int(11) DEFAULT NULL,
Alessandro Vullo's avatar
Alessandro Vullo committed
411
  `description` varchar(400) DEFAULT NULL,
412 413 414 415 416
  `url` varchar(255) DEFAULT NULL,
  `type` enum('chip','lsdb') DEFAULT NULL,
  `somatic_status` enum('germline','somatic','mixed') DEFAULT 'germline',
  `data_types` set('variation','variation_synonym','structural_variation','phenotype_feature','study') DEFAULT NULL,
  PRIMARY KEY (`source_id`)
417
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
418

419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
CREATE TABLE `structural_variation` (
  `structural_variation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `variation_name` varchar(255) DEFAULT NULL,
  `alias` varchar(255) DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `study_id` int(10) unsigned DEFAULT NULL,
  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
  `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
  `validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
  `is_evidence` tinyint(4) DEFAULT '0',
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
  `copy_number` tinyint(2) DEFAULT NULL,
  PRIMARY KEY (`structural_variation_id`),
  UNIQUE KEY `variation_name` (`variation_name`),
  KEY `source_idx` (`source_id`),
  KEY `study_idx` (`study_id`),
  KEY `attrib_idx` (`class_attrib_id`)
436
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
437

438 439 440 441 442 443
CREATE TABLE `structural_variation_association` (
  `structural_variation_id` int(10) unsigned NOT NULL,
  `supporting_structural_variation_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`structural_variation_id`,`supporting_structural_variation_id`),
  KEY `structural_variation_idx` (`structural_variation_id`),
  KEY `supporting_structural_variation_idx` (`supporting_structural_variation_id`)
Anja Thormann's avatar
Anja Thormann committed
444
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
445

446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473
CREATE TABLE `structural_variation_feature` (
  `structural_variation_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `seq_region_id` int(10) unsigned NOT NULL,
  `outer_start` int(11) DEFAULT NULL,
  `seq_region_start` int(11) NOT NULL,
  `inner_start` int(11) DEFAULT NULL,
  `inner_end` int(11) DEFAULT NULL,
  `seq_region_end` int(11) NOT NULL,
  `outer_end` int(11) DEFAULT NULL,
  `seq_region_strand` tinyint(4) NOT NULL,
  `structural_variation_id` int(10) unsigned NOT NULL,
  `variation_name` varchar(255) DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `study_id` int(10) unsigned DEFAULT NULL,
  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
  `allele_string` longtext,
  `is_evidence` tinyint(1) NOT NULL DEFAULT '0',
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
  `breakpoint_order` tinyint(4) DEFAULT NULL,
  `length` int(10) DEFAULT NULL,
  `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
  PRIMARY KEY (`structural_variation_feature_id`),
  KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
  KEY `structural_variation_idx` (`structural_variation_id`),
  KEY `source_idx` (`source_id`),
  KEY `study_idx` (`study_id`),
  KEY `attrib_idx` (`class_attrib_id`),
  KEY `variation_set_idx` (`variation_set_id`)
474
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
475

476 477 478 479
CREATE TABLE `structural_variation_sample` (
  `structural_variation_sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `structural_variation_id` int(10) unsigned NOT NULL,
  `sample_id` int(10) unsigned DEFAULT NULL,
480
  `zygosity` tinyint(1) DEFAULT NULL,
481 482 483
  PRIMARY KEY (`structural_variation_sample_id`),
  KEY `structural_variation_idx` (`structural_variation_id`),
  KEY `sample_idx` (`sample_id`)
Anja Thormann's avatar
Anja Thormann committed
484
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
485 486 487 488 489 490 491 492 493 494

CREATE TABLE `study` (
  `study_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  `description` text,
  `url` varchar(255) DEFAULT NULL,
  `external_reference` varchar(255) DEFAULT NULL,
  `study_type` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`study_id`),
495 496 497
  KEY `source_idx` (`source_id`),
  KEY `external_reference_idx` (`external_reference`)
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
498

499 500 501 502 503 504
CREATE TABLE `submitter` (
  `submitter_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `description` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`submitter_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

505 506 507 508 509
CREATE TABLE `submitter_handle` (
  `handle_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `handle` varchar(25) DEFAULT NULL,
  PRIMARY KEY (`handle_id`),
  UNIQUE KEY `handle` (`handle`)
510 511
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

512 513 514 515
CREATE TABLE `subsnp_handle` (
  `subsnp_id` int(11) unsigned NOT NULL,
  `handle` varchar(20) DEFAULT NULL,
  PRIMARY KEY (`subsnp_id`)
Anja Thormann's avatar
Anja Thormann committed
516
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
517 518

CREATE TABLE `tmp_sample_genotype_single_bp` (
519 520 521 522
  `variation_id` int(10) NOT NULL,
  `subsnp_id` int(15) unsigned DEFAULT NULL,
  `allele_1` char(1) DEFAULT NULL,
  `allele_2` char(1) DEFAULT NULL,
523
  `sample_id` int(10) unsigned NOT NULL,
524 525
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`),
526 527 528
  KEY `sample_idx` (`sample_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000;

529 530 531 532 533 534
CREATE TABLE `transcript_variation` (
  `transcript_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `variation_feature_id` int(11) unsigned NOT NULL,
  `feature_stable_id` varchar(128) DEFAULT NULL,
  `allele_string` text,
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
535
  `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556
  `cds_start` int(11) unsigned DEFAULT NULL,
  `cds_end` int(11) unsigned DEFAULT NULL,
  `cdna_start` int(11) unsigned DEFAULT NULL,
  `cdna_end` int(11) unsigned DEFAULT NULL,
  `translation_start` int(11) unsigned DEFAULT NULL,
  `translation_end` int(11) unsigned DEFAULT NULL,
  `distance_to_transcript` int(11) unsigned DEFAULT NULL,
  `codon_allele_string` text,
  `pep_allele_string` text,
  `hgvs_genomic` text,
  `hgvs_transcript` text,
  `hgvs_protein` text,
  `polyphen_prediction` enum('unknown','benign','possibly damaging','probably damaging') DEFAULT NULL,
  `polyphen_score` float DEFAULT NULL,
  `sift_prediction` enum('tolerated','deleterious','tolerated - low confidence','deleterious - low confidence') DEFAULT NULL,
  `sift_score` float DEFAULT NULL,
  `display` int(1) DEFAULT '1',
  PRIMARY KEY (`transcript_variation_id`),
  KEY `variation_feature_idx` (`variation_feature_id`),
  KEY `consequence_type_idx` (`consequence_types`),
  KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`)
Anja Thormann's avatar
Anja Thormann committed
557
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
558 559 560 561 562 563

CREATE TABLE `translation_md5` (
  `translation_md5_id` int(11) NOT NULL AUTO_INCREMENT,
  `translation_md5` char(32) NOT NULL,
  PRIMARY KEY (`translation_md5_id`),
  UNIQUE KEY `md5_idx` (`translation_md5`)
Anja Thormann's avatar
Anja Thormann committed
564
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
565 566 567 568 569 570 571 572 573 574 575 576 577

CREATE TABLE `variation` (
  `variation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  `ancestral_allele` varchar(255) DEFAULT NULL,
  `flipped` tinyint(1) unsigned DEFAULT NULL,
  `class_attrib_id` int(10) unsigned DEFAULT '0',
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
  `minor_allele` varchar(50) DEFAULT NULL,
  `minor_allele_freq` float DEFAULT NULL,
  `minor_allele_count` int(10) unsigned DEFAULT NULL,
  `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
578
  `evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
579 580 581 582
  `display` int(1) DEFAULT '1',
  PRIMARY KEY (`variation_id`),
  UNIQUE KEY `name` (`name`),
  KEY `source_idx` (`source_id`)
583
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
584 585 586 587 588 589 590

CREATE TABLE `variation_attrib` (
  `variation_id` int(11) unsigned NOT NULL,
  `attrib_id` int(11) DEFAULT NULL,
  `value` varchar(255) DEFAULT NULL,
  KEY `variation_idx` (`variation_id`),
  KEY `attrib_value_idx` (`attrib_id`,`value`)
Anja Thormann's avatar
Anja Thormann committed
591
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
592 593 594 595 596

CREATE TABLE `variation_citation` (
  `variation_id` int(10) unsigned NOT NULL,
  `publication_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`variation_id`,`publication_id`)
Anja Thormann's avatar
Anja Thormann committed
597
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
598 599 600 601 602 603 604 605 606 607 608 609 610

CREATE TABLE `variation_feature` (
  `variation_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `seq_region_id` int(10) unsigned NOT NULL,
  `seq_region_start` int(11) NOT NULL,
  `seq_region_end` int(11) NOT NULL,
  `seq_region_strand` tinyint(4) NOT NULL,
  `variation_id` int(10) unsigned NOT NULL,
  `allele_string` varchar(50000) DEFAULT NULL,
  `variation_name` varchar(255) DEFAULT NULL,
  `map_weight` int(11) NOT NULL,
  `flags` set('genotyped') DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
611
  `consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
612 613 614 615 616 617 618
  `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
  `class_attrib_id` int(10) unsigned DEFAULT '0',
  `somatic` tinyint(1) NOT NULL DEFAULT '0',
  `minor_allele` varchar(50) DEFAULT NULL,
  `minor_allele_freq` float DEFAULT NULL,
  `minor_allele_count` int(10) unsigned DEFAULT NULL,
  `alignment_quality` double DEFAULT NULL,
619
  `evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
620
  `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
621 622 623 624 625 626 627
  `display` int(1) DEFAULT '1',
  PRIMARY KEY (`variation_feature_id`),
  KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
  KEY `variation_idx` (`variation_id`),
  KEY `variation_set_idx` (`variation_set_id`),
  KEY `consequence_type_idx` (`consequence_types`),
  KEY `source_idx` (`source_id`)
628
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
629

630 631 632 633
CREATE TABLE `variation_genename` (
  `variation_id` int(10) unsigned NOT NULL,
  `gene_name` varchar(255) NOT NULL,
  PRIMARY KEY (`variation_id`,`gene_name`)
Anja Thormann's avatar
Anja Thormann committed
634
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
635

636 637 638 639
CREATE TABLE `variation_hgvs` (
  `variation_id` int(10) unsigned NOT NULL,
  `hgvs_name` varchar(255) NOT NULL,
  PRIMARY KEY (`variation_id`,`hgvs_name`)
Anja Thormann's avatar
Anja Thormann committed
640
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
641

642 643 644 645 646 647 648
CREATE TABLE `variation_set` (
  `variation_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `description` text,
  `short_name_attrib_id` int(10) unsigned DEFAULT NULL,
  PRIMARY KEY (`variation_set_id`),
  KEY `name_idx` (`name`)
649
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
650

651 652 653 654
CREATE TABLE `variation_set_structural_variation` (
  `structural_variation_id` int(10) unsigned NOT NULL,
  `variation_set_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`structural_variation_id`,`variation_set_id`)
Anja Thormann's avatar
Anja Thormann committed
655
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
656

657 658 659 660 661
CREATE TABLE `variation_set_structure` (
  `variation_set_super` int(10) unsigned NOT NULL,
  `variation_set_sub` int(10) unsigned NOT NULL,
  PRIMARY KEY (`variation_set_super`,`variation_set_sub`),
  KEY `sub_idx` (`variation_set_sub`,`variation_set_super`)
Anja Thormann's avatar
Anja Thormann committed
662
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
663 664 665 666 667 668

CREATE TABLE `variation_set_variation` (
  `variation_id` int(10) unsigned NOT NULL,
  `variation_set_id` int(10) unsigned NOT NULL,
  PRIMARY KEY (`variation_id`,`variation_set_id`),
  KEY `variation_set_idx` (`variation_set_id`,`variation_id`)
Anja Thormann's avatar
Anja Thormann committed
669
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
670 671 672 673 674 675 676 677 678 679 680 681

CREATE TABLE `variation_synonym` (
  `variation_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `variation_id` int(10) unsigned NOT NULL,
  `subsnp_id` int(15) unsigned DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  PRIMARY KEY (`variation_synonym_id`),
  UNIQUE KEY `name` (`name`,`source_id`),
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`),
  KEY `source_idx` (`source_id`)
Anja Thormann's avatar
Anja Thormann committed
682
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
683