Unverified Commit 052d23be authored by Marek Szuba's avatar Marek Szuba Committed by GitHub
Browse files

Merge pull request #87 from Ensembl/rel98_variation_testdb

Patch the variation test database to version 98 [release/98]
parents 33b92e78 1987aaae
1 \N schema_type variation
2 \N schema_version 96
2 \N schema_version 98
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
......@@ -39,3 +39,7 @@
39 \N patch patch_95_96_c.sql|add new entries to the failed_description table
40 \N patch patch_95_96_d.sql|create table to store failed variation features
41 \N patch patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.
42 \N patch patch_96_97_a.sql|schema version
43 \N patch patch_96_97_b.sql|move ancestral allele column to variation_feature
44 \N patch patch_96_97_c.sql|add an unique index on the name column
45 \N patch patch_97_98_a.sql|schema version
......@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` (
CREATE TABLE `attrib` (
`attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`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))
) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_set` (
`attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
`attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
`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`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text,
`description` text DEFAULT NULL,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` (
`seq_region_start` int(11) NOT NULL,
`seq_region_end` int(11) NOT NULL,
`seq_region_strand` tinyint(4) NOT NULL,
`genotypes` blob,
`genotypes` blob DEFAULT NULL,
KEY `pos_idx` (`seq_region_id`,`seq_region_start`),
KEY `sample_idx` (`sample_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` (
CREATE TABLE `compressed_genotype_var` (
`variation_id` int(11) unsigned NOT NULL,
`subsnp_id` int(11) unsigned DEFAULT NULL,
`genotypes` blob,
`genotypes` blob DEFAULT NULL,
KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned NOT NULL DEFAULT '1',
`species_id` int(10) unsigned NOT NULL DEFAULT 1,
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
......@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` (
CREATE TABLE `individual` (
`individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
`description` text,
`description` text DEFAULT NULL,
`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',
`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`)
......@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` (
CREATE TABLE `individual_type` (
`individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) NOT NULL,
`description` text,
`description` text DEFAULT NULL,
PRIMARY KEY (`individual_type_id`)
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`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`)
) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=46 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` (
`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',
`allele_string` text DEFAULT NULL,
`somatic` tinyint(1) NOT NULL DEFAULT 0,
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`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',
`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`),
......@@ -233,7 +233,7 @@ CREATE TABLE `phenotype_feature` (
`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',
`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,
......@@ -267,8 +267,8 @@ 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',
`description` text DEFAULT NULL,
`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,
......@@ -310,7 +310,7 @@ CREATE TABLE `population_synonym` (
CREATE TABLE `protein_function_predictions` (
`translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL,
`prediction_matrix` mediumblob,
`prediction_matrix` mediumblob DEFAULT NULL,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -318,7 +318,7 @@ 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,
`position_values` blob DEFAULT NULL,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -350,9 +350,9 @@ 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',
`feature_type` text DEFAULT NULL,
`allele_string` text DEFAULT NULL,
`somatic` tinyint(1) NOT NULL DEFAULT 0,
`consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL,
PRIMARY KEY (`regulatory_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
......@@ -365,10 +365,10 @@ 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,
`description` text DEFAULT NULL,
`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',
`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`),
KEY `individual_idx` (`individual_id`),
......@@ -421,7 +421,8 @@ CREATE TABLE `source` (
`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`)
PRIMARY KEY (`source_id`),
UNIQUE KEY `name_idx` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
CREATE TABLE `structural_variation` (
......@@ -430,11 +431,11 @@ CREATE TABLE `structural_variation` (
`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',
`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',
`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`),
......@@ -465,10 +466,10 @@ CREATE TABLE `structural_variation_feature` (
`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',
`class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
`allele_string` longtext DEFAULT NULL,
`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 '',
......@@ -495,7 +496,7 @@ 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,
`description` text DEFAULT NULL,
`url` varchar(255) DEFAULT NULL,
`external_reference` varchar(255) DEFAULT NULL,
`study_type` varchar(255) DEFAULT NULL,
......@@ -538,8 +539,8 @@ 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',
`allele_string` text DEFAULT NULL,
`somatic` tinyint(1) NOT NULL DEFAULT 0,
`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,
`cds_start` int(11) unsigned DEFAULT NULL,
`cds_end` int(11) unsigned DEFAULT NULL,
......@@ -548,16 +549,16 @@ CREATE TABLE `transcript_variation` (
`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,
`codon_allele_string` text DEFAULT NULL,
`pep_allele_string` text DEFAULT NULL,
`hgvs_genomic` text DEFAULT NULL,
`hgvs_transcript` text DEFAULT NULL,
`hgvs_protein` text DEFAULT NULL,
`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',
`display` int(1) DEFAULT 1,
PRIMARY KEY (`transcript_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
......@@ -575,16 +576,15 @@ 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',
`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,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`display` int(1) DEFAULT '1',
`display` int(1) DEFAULT 1,
PRIMARY KEY (`variation_id`),
UNIQUE KEY `name` (`name`),
KEY `source_idx` (`source_id`)
......@@ -612,21 +612,22 @@ CREATE TABLE `variation_feature` (
`seq_region_strand` tinyint(4) NOT NULL,
`variation_id` int(10) unsigned NOT NULL,
`allele_string` varchar(50000) DEFAULT NULL,
`ancestral_allele` varchar(50) 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,
`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',
`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',
`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,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') 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,
`display` int(1) DEFAULT '1',
`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`),
......@@ -650,7 +651,7 @@ CREATE TABLE `variation_hgvs` (
CREATE TABLE `variation_set` (
`variation_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
`description` text,
`description` text DEFAULT NULL,
`short_name_attrib_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`variation_set_id`),
KEY `name_idx` (`name`)
......
1 1 rs12345 \N \N 0 0 \N \N \N \N \N 1
2 1 rs67890 \N \N 0 0 \N \N \N \N \N 1
3 1 rs54321 \N \N 0 1 \N \N \N \N \N 1
1 1 rs12345 \N 0 0 \N \N \N \N \N 1
2 1 rs67890 \N 0 0 \N \N \N \N \N 1
3 1 rs54321 \N 0 1 \N \N \N \N \N 1
1 469283 30252800 30252800 1 1 \N rs12345 1 genotyped 1 intergenic_variant 1 0 0 \N \N \N \N \N \N 1
2 469283 30252900 30252900 1 2 \N rs67890 1 \N 1 intergenic_variant 1 0 0 \N \N \N \N \N \N 1
3 469283 30253900 30253900 1 3 \N rs54321 1 \N 1 intergenic_variant 0 1 \N \N \N \N \N \N 1
1 469283 30252800 30252800 1 1 \N \N rs12345 1 genotyped 1 intergenic_variant 1 0 0 \N \N \N \N \N \N 1
2 469283 30252900 30252900 1 2 \N \N rs67890 1 \N 1 intergenic_variant 1 0 0 \N \N \N \N \N \N 1
3 469283 30253900 30253900 1 3 \N \N rs54321 1 \N 1 intergenic_variant 0 1 \N \N \N \N \N \N 1
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