diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index dd2765e241160639e47b2e500405052de11ce5f5..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -19,66 +19,67 @@ CREATE TABLE `alt_allele_group` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=InnoDB AUTO_INCREMENT=39 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` varchar(128) DEFAULT NULL,
PRIMARY KEY (`associated_group_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -94,16 +95,16 @@ CREATE TABLE `associated_xref` (
KEY `associated_object_idx` (`object_xref_id`),
KEY `associated_idx` (`xref_id`),
KEY `associated_group_idx` (`associated_group_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB AUTO_INCREMENT=391 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -131,29 +132,29 @@ CREATE TABLE `data_file` (
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
KEY `df_analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -162,16 +163,16 @@ CREATE TABLE `dependent_xref` (
PRIMARY KEY (`object_xref_id`),
KEY `dependent` (`dependent_xref_id`),
KEY `master_idx` (`master_xref_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,38 +242,37 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL','IGNORE','ALT_GENE') DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
- PRIMARY KEY (`external_db_id`),
- UNIQUE KEY `db_name_idx` (`db_name`,`db_release`)
-) ENGINE=InnoDB AUTO_INCREMENT=50745 DEFAULT CHARSET=latin1;
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -285,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -297,24 +296,22 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -322,9 +319,8 @@ CREATE TABLE `gene_attrib` (
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `gene_idx` (`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -339,25 +335,25 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -373,27 +369,27 @@ CREATE TABLE `intron_supporting_evidence` (
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -401,9 +397,8 @@ CREATE TABLE `mapping_session` (
`old_assembly` varchar(20) NOT NULL DEFAULT '',
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
- `species_id` int(10) NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -411,72 +406,71 @@ CREATE TABLE `mapping_set` (
`external_schema_build` varchar(20) NOT NULL,
PRIMARY KEY (`mapping_set_id`),
UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=InnoDB AUTO_INCREMENT=97 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -484,9 +478,8 @@ CREATE TABLE `misc_attrib` (
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -496,46 +489,45 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source_xref_id` int(10) unsigned DEFAULT NULL,
`linkage_type` varchar(3) DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`),
- KEY `object_idx` (`object_xref_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
`operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -553,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -572,66 +564,66 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
`gene_id` int(10) unsigned DEFAULT NULL,
KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -639,68 +631,68 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `translation_idx` (`translation_id`),
- KEY `hitname_idx` (`hit_name`),
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=14 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -708,62 +700,60 @@ CREATE TABLE `seq_region_attrib` (
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `mapping_set_id` (`mapping_set_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=InnoDB AUTO_INCREMENT=37 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -776,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -791,7 +781,7 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -799,9 +789,8 @@ CREATE TABLE `transcript_attrib` (
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -810,15 +799,15 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
`next_exon_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -834,7 +823,7 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -842,15 +831,14 @@ CREATE TABLE `translation_attrib` (
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `translation_idx` (`translation_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -859,31 +847,30 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
- KEY `id_idx` (`identifier`(50)),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
- KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=InnoDB AUTO_INCREMENT=91703 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 0d3e49810a7eecad14024bdae78e250c749fea53..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
PRIMARY KEY (`alt_allele_id`),
UNIQUE KEY `gene_idx` (`gene_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,63 +16,64 @@ CREATE TABLE `alt_allele_attrib` (
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=8412 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -100,10 +101,10 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=20 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -131,29 +132,29 @@ CREATE TABLE `data_file` (
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
KEY `df_analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float(8,2) NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=319 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -165,13 +166,13 @@ CREATE TABLE `dependent_xref` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3278359 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
-) ENGINE=MyISAM AUTO_INCREMENT=4828764 DEFAULT CHARSET=latin1;
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=29797194 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,38 +242,37 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=162051 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
- PRIMARY KEY (`external_db_id`),
- UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
-) ENGINE=MyISAM AUTO_INCREMENT=11001 DEFAULT CHARSET=latin1;
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -285,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -297,34 +296,31 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=18284 DEFAULT CHARSET=latin1;
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
- KEY `gene_idx` (`gene_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -339,25 +335,25 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -373,27 +369,27 @@ CREATE TABLE `intron_supporting_evidence` (
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=6 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -402,7 +398,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -415,77 +411,75 @@ CREATE TABLE `mapping_set` (
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=102 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=136 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
- KEY `misc_feature_idx` (`misc_feature_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `misc_feature_idx` (`misc_feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -495,45 +489,44 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=253693 DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`),
- KEY `object_idx` (`object_xref_id`)
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
@@ -552,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -571,7 +564,7 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -580,57 +573,57 @@ CREATE TABLE `operon_transcript_gene` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=194 DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=18085 DEFAULT CHARSET=latin1;
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -638,131 +631,129 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11554507 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double(8,2) DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `translation_idx` (`translation_id`),
- KEY `hitname_idx` (`hit_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=242848 DEFAULT CHARSET=latin1;
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1020 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=922516 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=965911 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
- KEY `seq_region_idx` (`seq_region_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
+ KEY `mapping_set_id` (`mapping_set_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -775,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -790,17 +781,16 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21752 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
- KEY `transcript_idx` (`transcript_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -812,12 +802,12 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -833,23 +823,22 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21747 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
- KEY `translation_idx` (`translation_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -858,31 +847,30 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
- KEY `id_idx` (`identifier`(50)),
- KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1000007 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index 616a914147708afc6264dd00f3d9278d48a79bc5..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
@@ -36,16 +36,16 @@ CREATE TABLE `analysis` (
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name` (`logic_name`),
KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
- `description` text,
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
+ `web_data` text COLLATE latin1_bin,
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
`asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -58,7 +58,7 @@ CREATE TABLE `assembly` (
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -73,7 +73,7 @@ CREATE TABLE `assembly_exception` (
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -101,10 +101,10 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -144,7 +144,7 @@ CREATE TABLE `density_feature` (
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -154,7 +154,7 @@ CREATE TABLE `density_type` (
`value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -197,7 +197,7 @@ CREATE TABLE `dna` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -213,17 +213,17 @@ CREATE TABLE `dna_align_feature` (
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -251,7 +251,7 @@ CREATE TABLE `exon_transcript` (
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
`external_db_id` int(11) NOT NULL DEFAULT '0',
@@ -263,16 +263,16 @@ CREATE TABLE `external_db` (
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
`xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -297,7 +297,7 @@ CREATE TABLE `gene` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) NOT NULL DEFAULT '',
@@ -311,7 +311,7 @@ CREATE TABLE `gene_archive` (
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -319,9 +319,8 @@ CREATE TABLE `gene_attrib` (
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `gene_idx` (`gene_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -343,18 +342,18 @@ CREATE TABLE `identity_xref` (
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
`interpro_ac` varchar(40) NOT NULL DEFAULT '',
`id` varchar(40) NOT NULL DEFAULT '',
UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
KEY `id` (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -368,8 +367,9 @@ CREATE TABLE `intron_supporting_evidence` (
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
`is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
- UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -380,13 +380,13 @@ CREATE TABLE `karyotype` (
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
`mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -398,7 +398,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -419,7 +419,7 @@ CREATE TABLE `marker` (
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -432,7 +432,7 @@ CREATE TABLE `marker_feature` (
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
`marker_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -443,7 +443,7 @@ CREATE TABLE `marker_map_location` (
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -453,7 +453,7 @@ CREATE TABLE `marker_synonym` (
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -463,14 +463,14 @@ CREATE TABLE `meta` (
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=125 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL DEFAULT '',
`coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -478,9 +478,8 @@ CREATE TABLE `misc_attrib` (
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -490,14 +489,14 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
@@ -507,19 +506,19 @@ CREATE TABLE `misc_set` (
`max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -579,7 +578,7 @@ CREATE TABLE `peptide_archive` (
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -595,7 +594,7 @@ CREATE TABLE `prediction_exon` (
PRIMARY KEY (`prediction_exon_id`),
KEY `prediction_transcript_id` (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -608,7 +607,7 @@ CREATE TABLE `prediction_transcript` (
PRIMARY KEY (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -623,7 +622,7 @@ CREATE TABLE `protein_align_feature` (
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
@@ -632,7 +631,7 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -646,27 +645,27 @@ CREATE TABLE `protein_feature` (
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
KEY `translation_id` (`translation_id`),
KEY `hitname_index` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`repeat_name` varchar(255) NOT NULL DEFAULT '',
`repeat_class` varchar(100) NOT NULL DEFAULT '',
`repeat_type` varchar(40) NOT NULL DEFAULT '',
- `repeat_consensus` text,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -683,7 +682,7 @@ CREATE TABLE `repeat_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -693,7 +692,7 @@ CREATE TABLE `seq_region` (
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
KEY `name_idx` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -701,9 +700,8 @@ CREATE TABLE `seq_region_attrib` (
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
@@ -719,7 +717,7 @@ CREATE TABLE `seq_region_synonym` (
`external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -734,7 +732,7 @@ CREATE TABLE `simple_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
@@ -747,7 +745,7 @@ CREATE TABLE `stable_id_event` (
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
`exon_id` int(11) NOT NULL DEFAULT '0',
@@ -755,7 +753,7 @@ CREATE TABLE `supporting_feature` (
`feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -783,7 +781,7 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -791,9 +789,8 @@ CREATE TABLE `transcript_attrib` (
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -810,7 +807,7 @@ CREATE TABLE `transcript_supporting_feature` (
`feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -834,9 +831,8 @@ CREATE TABLE `translation_attrib` (
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `translation_idx` (`translation_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -849,30 +845,32 @@ CREATE TABLE `unmapped_object` (
`target_score` double DEFAULT NULL,
`ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
+ `parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
KEY `id_idx` (`identifier`),
KEY `anal_idx` (`analysis_id`),
KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
- KEY `display_index` (`display_label`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `display_index` (`display_label`),
+ KEY `info_type_idx` (`info_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
index ab24bfa198316cf3ed7f46046c69d78a8fdba7f8..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
PRIMARY KEY (`alt_allele_id`),
UNIQUE KEY `gene_idx` (`gene_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,32 +16,32 @@ CREATE TABLE `alt_allele_attrib` (
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=5213 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
`analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
- `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
- `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
+ `db` varchar(120) DEFAULT NULL,
+ `db_version` varchar(40) DEFAULT NULL,
+ `db_file` varchar(120) DEFAULT NULL,
+ `program` varchar(80) DEFAULT NULL,
+ `program_version` varchar(40) DEFAULT NULL,
+ `program_file` varchar(80) DEFAULT NULL,
`parameters` text COLLATE latin1_bin,
- `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `module` varchar(80) DEFAULT NULL,
+ `module_version` varchar(40) DEFAULT NULL,
+ `gff_source` varchar(40) DEFAULT NULL,
+ `gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name` (`logic_name`),
KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=8451 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`description` text COLLATE latin1_bin,
- `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
`web_data` text COLLATE latin1_bin,
KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
`seq_region_id` int(11) NOT NULL DEFAULT '0',
`seq_region_start` int(11) NOT NULL DEFAULT '0',
`seq_region_end` int(11) NOT NULL DEFAULT '0',
- `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
`exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
`exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
`exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -73,7 +73,7 @@ CREATE TABLE `assembly_exception` (
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=157 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
- `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `code` varchar(20) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=405 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1004 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -144,17 +144,17 @@ CREATE TABLE `density_feature` (
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=16758826 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
`analysis_id` int(11) NOT NULL DEFAULT '0',
`block_size` int(11) NOT NULL DEFAULT '0',
`region_features` int(11) NOT NULL DEFAULT '0',
- `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM AUTO_INCREMENT=110 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -172,7 +172,7 @@ CREATE TABLE `ditag` (
`tag_count` smallint(6) DEFAULT '1',
`sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -191,11 +191,11 @@ CREATE TABLE `ditag_feature` (
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4828763 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `sequence` mediumtext COLLATE latin1_bin NOT NULL,
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
`hit_start` int(11) NOT NULL DEFAULT '0',
`hit_end` int(11) NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
@@ -223,7 +223,7 @@ CREATE TABLE `dna_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=29797338 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=7296966 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
CREATE TABLE `external_db` (
`external_db_id` int(11) NOT NULL DEFAULT '0',
- `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
- `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
`priority` int(11) NOT NULL DEFAULT '0',
- `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
- `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `db_display_name` varchar(255) DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
+ `secondary_db_name` varchar(255) DEFAULT NULL,
+ `secondary_db_table` varchar(255) DEFAULT NULL,
`description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
`xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -297,14 +297,14 @@ CREATE TABLE `gene` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=633706 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
`gene_version` smallint(6) NOT NULL DEFAULT '0',
- `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
`transcript_version` smallint(6) NOT NULL DEFAULT '0',
- `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
`translation_version` smallint(6) NOT NULL DEFAULT '0',
`peptide_archive_id` int(11) NOT NULL DEFAULT '0',
`mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text COLLATE latin1_bin NOT NULL,
+ `value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
KEY `gene_idx` (`gene_id`)
@@ -332,7 +332,7 @@ CREATE TABLE `genome_statistics` (
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
KEY `id` (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,29 +376,29 @@ CREATE TABLE `karyotype` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_start` int(10) NOT NULL DEFAULT '0',
`seq_region_end` int(10) NOT NULL DEFAULT '0',
- `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `band` varchar(40) DEFAULT NULL,
+ `stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=852 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
`mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
- `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
- `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
- `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
- `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
- `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
- `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_db_name` varchar(80) NOT NULL DEFAULT '',
+ `new_db_name` varchar(80) NOT NULL DEFAULT '',
+ `old_release` varchar(5) NOT NULL DEFAULT '',
+ `new_release` varchar(5) NOT NULL DEFAULT '',
+ `old_assembly` varchar(20) NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=394 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -411,15 +411,15 @@ CREATE TABLE `mapping_set` (
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
`min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
- `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -432,14 +432,14 @@ CREATE TABLE `marker_feature` (
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
`marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_id` int(10) unsigned NOT NULL DEFAULT '0',
- `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
`marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
- `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,12 +448,12 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`marker_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
- `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
+ `source` varchar(20) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=716771 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
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=2088 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `table_name` varchar(40) NOT NULL DEFAULT '',
`coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text COLLATE latin1_bin NOT NULL,
+ `value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
KEY `misc_feature_idx` (`misc_feature_id`)
@@ -489,7 +489,7 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=93001 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -500,25 +500,25 @@ CREATE TABLE `misc_feature_misc_set` (
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
- `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin NOT NULL,
+ `code` varchar(25) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text NOT NULL,
`max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
- `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `linkage_annotation` varchar(255) DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=17375428 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -545,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -564,7 +564,7 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -574,11 +574,11 @@ CREATE TABLE `operon_transcript_gene` (
CREATE TABLE `peptide_archive` (
`peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
- `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
- `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
+ `md5_checksum` varchar(32) DEFAULT NULL,
+ `peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=250655 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -594,7 +594,7 @@ CREATE TABLE `prediction_exon` (
PRIMARY KEY (`prediction_exon_id`),
KEY `prediction_transcript_id` (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=394607 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -603,11 +603,11 @@ CREATE TABLE `prediction_transcript` (
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
- `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=54799 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
- `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
@@ -631,7 +631,7 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=19573639 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
- `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
@@ -652,20 +652,20 @@ CREATE TABLE `protein_feature` (
KEY `translation_id` (`translation_id`),
KEY `hitname_index` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=7821872 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
`repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=595635 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,22 +682,22 @@ CREATE TABLE `repeat_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=31576665 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(40) NOT NULL DEFAULT '',
`coord_system_id` int(10) NOT NULL DEFAULT '0',
`length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
KEY `name_idx` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=1001161224 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text COLLATE latin1_bin NOT NULL,
+ `value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
KEY `seq_region_idx` (`seq_region_id`)
@@ -717,7 +717,7 @@ CREATE TABLE `seq_region_synonym` (
`external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=177 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -725,22 +725,22 @@ CREATE TABLE `simple_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=968567 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
- `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
- `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
`mapping_session_id` int(10) NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
CREATE TABLE `supporting_feature` (
`exon_id` int(11) NOT NULL DEFAULT '0',
- `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
+ `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
`feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -781,12 +781,12 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=2047853 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text COLLATE latin1_bin NOT NULL,
+ `value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
CREATE TABLE `transcript_supporting_feature` (
`transcript_id` int(11) NOT NULL DEFAULT '0',
- `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
+ `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
`feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -823,12 +823,12 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=1044748 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text COLLATE latin1_bin NOT NULL,
+ `value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
KEY `translation_idx` (`translation_id`)
@@ -836,41 +836,41 @@ CREATE TABLE `translation_attrib` (
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
+ `type` enum('xref','cDNA','Marker') NOT NULL,
`analysis_id` int(10) unsigned NOT NULL,
`external_db_id` int(11) DEFAULT NULL,
- `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
+ `identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
`ensembl_id` int(10) unsigned DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
- `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
+ `parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
KEY `id_idx` (`identifier`),
KEY `anal_idx` (`analysis_id`),
KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=12401901 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `summary_description` varchar(255) DEFAULT NULL,
+ `full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`external_db_id` int(11) NOT NULL,
- `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
- `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
- `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
+ `dbprimary_acc` varchar(512) NOT NULL,
+ `display_label` varchar(512) NOT NULL,
+ `version` varchar(10) DEFAULT NULL,
`description` text COLLATE latin1_bin,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
- `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=7795492 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/mapping/core/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index 08c7a3f90d1f3f4fc738da6361719a2d7a142f75..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
PRIMARY KEY (`alt_allele_id`),
UNIQUE KEY `gene_idx` (`gene_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,63 +16,64 @@ CREATE TABLE `alt_allele_attrib` (
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=8409 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -100,10 +101,10 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -134,26 +135,26 @@ CREATE TABLE `data_file` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float(8,2) NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -165,13 +166,13 @@ CREATE TABLE `dependent_xref` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
-) ENGINE=MyISAM AUTO_INCREMENT=4828763 DEFAULT CHARSET=latin1;
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=29797140 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,38 +242,37 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=162034 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
- PRIMARY KEY (`external_db_id`),
- UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
-) ENGINE=MyISAM AUTO_INCREMENT=4201 DEFAULT CHARSET=latin1;
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -285,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -297,34 +296,31 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=18276 DEFAULT CHARSET=latin1;
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
- KEY `gene_idx` (`gene_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -339,25 +335,25 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -377,23 +373,23 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -402,7 +398,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -415,77 +411,75 @@ CREATE TABLE `mapping_set` (
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=130 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
- KEY `misc_feature_idx` (`misc_feature_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `misc_feature_idx` (`misc_feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -495,45 +489,44 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=253685 DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`),
- KEY `object_idx` (`object_xref_id`)
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
@@ -552,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -571,7 +564,7 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -580,57 +573,57 @@ CREATE TABLE `operon_transcript_gene` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=192 DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=18084 DEFAULT CHARSET=latin1;
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -638,131 +631,129 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11554505 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double(8,2) DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `translation_idx` (`translation_id`),
- KEY `hitname_idx` (`hit_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=242847 DEFAULT CHARSET=latin1;
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1018 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=922515 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
- KEY `seq_region_idx` (`seq_region_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
+ KEY `mapping_set_id` (`mapping_set_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -775,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -790,17 +781,16 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21741 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
- KEY `transcript_idx` (`transcript_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -812,12 +802,12 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -833,23 +823,22 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21741 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
- KEY `translation_idx` (`translation_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -858,31 +847,30 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
- KEY `id_idx` (`identifier`(50)),
- KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1000000 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index 723cf3abd607f586225807847d0f62f7cd08a2f1..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
@@ -19,60 +19,61 @@ CREATE TABLE `alt_allele_group` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -100,10 +101,10 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=508 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=112 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -134,26 +135,26 @@ CREATE TABLE `data_file` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -165,11 +166,11 @@ CREATE TABLE `dependent_xref` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL DEFAULT '',
- `type` varchar(30) NOT NULL DEFAULT '',
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`)
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -245,36 +245,34 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `dbprimary_acc_linkable` tinyint(1) NOT NULL DEFAULT '1',
- `display_label_linkable` tinyint(1) NOT NULL DEFAULT '0',
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -286,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -298,33 +296,31 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+ KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
- KEY `peptide_archive_id_idx` (`peptide_archive_id`),
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
+ UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `gene_idx` (`gene_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -339,25 +335,25 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -377,23 +373,23 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -402,7 +398,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -415,76 +411,75 @@ CREATE TABLE `mapping_set` (
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=1666 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
+ UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -494,44 +489,44 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source_xref_id` int(10) unsigned DEFAULT NULL,
`linkage_type` varchar(3) DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`)
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
@@ -578,57 +573,57 @@ CREATE TABLE `operon_transcript_gene` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -636,129 +631,129 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `hitname_idx` (`hit_name`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `translation_idx` (`translation_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=20603 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
+ UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
+ KEY `mapping_set_id` (`mapping_set_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`)
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -771,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -792,10 +787,10 @@ CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
+ UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -807,12 +802,12 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -834,16 +829,16 @@ CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
+ UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `translation_idx` (`translation_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -853,28 +848,29 @@ CREATE TABLE `unmapped_object` (
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned DEFAULT NULL,
- `dbprimary_acc` varchar(50) NOT NULL,
- `display_label` varchar(128) NOT NULL,
+ `external_db_id` int(11) NOT NULL,
+ `dbprimary_acc` varchar(512) NOT NULL,
+ `display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index c300c2942678d0c74493c5310e7293f8648278bf..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
PRIMARY KEY (`alt_allele_id`),
UNIQUE KEY `gene_idx` (`gene_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,63 +16,64 @@ CREATE TABLE `alt_allele_attrib` (
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=8414 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -100,10 +101,10 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=20 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -131,29 +132,29 @@ CREATE TABLE `data_file` (
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
KEY `df_analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float(8,2) NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=319 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -165,13 +166,13 @@ CREATE TABLE `dependent_xref` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3278359 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
-) ENGINE=MyISAM AUTO_INCREMENT=4828764 DEFAULT CHARSET=latin1;
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=29797194 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,38 +242,37 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=162051 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
- PRIMARY KEY (`external_db_id`),
- UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
-) ENGINE=MyISAM AUTO_INCREMENT=4201 DEFAULT CHARSET=latin1;
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -285,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -297,34 +296,31 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=18284 DEFAULT CHARSET=latin1;
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
- KEY `gene_idx` (`gene_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -339,25 +335,25 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -373,27 +369,27 @@ CREATE TABLE `intron_supporting_evidence` (
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=6 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -402,7 +398,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -415,77 +411,75 @@ CREATE TABLE `mapping_set` (
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=102 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=129 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
- KEY `misc_feature_idx` (`misc_feature_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `misc_feature_idx` (`misc_feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -495,45 +489,44 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=253694 DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`),
- KEY `object_idx` (`object_xref_id`)
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
@@ -552,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -571,7 +564,7 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -580,57 +573,57 @@ CREATE TABLE `operon_transcript_gene` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=194 DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=18085 DEFAULT CHARSET=latin1;
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -638,131 +631,129 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11554507 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double(8,2) DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `translation_idx` (`translation_id`),
- KEY `hitname_idx` (`hit_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=242848 DEFAULT CHARSET=latin1;
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1020 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=922516 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=965911 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
- KEY `seq_region_idx` (`seq_region_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
+ KEY `mapping_set_id` (`mapping_set_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -775,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -790,17 +781,16 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21752 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
- KEY `transcript_idx` (`transcript_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -812,12 +802,12 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -833,23 +823,22 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21747 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
- KEY `translation_idx` (`translation_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -858,31 +847,30 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
- KEY `id_idx` (`identifier`(50)),
- KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1000008 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index 9946a1212498e78f244c1204fe7e83016cb99de7..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
PRIMARY KEY (`alt_allele_id`),
UNIQUE KEY `gene_idx` (`gene_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,63 +16,64 @@ CREATE TABLE `alt_allele_attrib` (
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=8412 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -100,10 +101,10 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=437 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -131,29 +132,29 @@ CREATE TABLE `data_file` (
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
KEY `df_analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float(8,2) NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=319 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM AUTO_INCREMENT=23 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -165,13 +166,13 @@ CREATE TABLE `dependent_xref` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3278359 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
-) ENGINE=MyISAM AUTO_INCREMENT=4828764 DEFAULT CHARSET=latin1;
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=29797194 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,38 +242,37 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=382467 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
- PRIMARY KEY (`external_db_id`),
- UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
-) ENGINE=MyISAM AUTO_INCREMENT=4201 DEFAULT CHARSET=latin1;
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -285,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -297,34 +296,31 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=40234 DEFAULT CHARSET=latin1;
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
- KEY `gene_idx` (`gene_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -336,28 +332,28 @@ CREATE TABLE `genome_statistics` (
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -373,27 +369,27 @@ CREATE TABLE `intron_supporting_evidence` (
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=6 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -402,7 +398,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -415,77 +411,75 @@ CREATE TABLE `mapping_set` (
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=102 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=210 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
- KEY `misc_feature_idx` (`misc_feature_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `misc_feature_idx` (`misc_feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -495,45 +489,44 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=24 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=253693 DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`),
- KEY `object_idx` (`object_xref_id`)
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
@@ -552,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -571,7 +564,7 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -580,57 +573,57 @@ CREATE TABLE `operon_transcript_gene` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=194 DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM AUTO_INCREMENT=18085 DEFAULT CHARSET=latin1;
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -638,131 +631,129 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11554507 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double(8,2) DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `analysis_idx` (`analysis_id`),
- KEY `translation_idx` (`translation_id`),
- KEY `hitname_idx` (`hit_name`)
-) ENGINE=MyISAM AUTO_INCREMENT=3502933 DEFAULT CHARSET=latin1;
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1163919 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=10446798 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3495795 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
- KEY `seq_region_idx` (`seq_region_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
+ KEY `mapping_set_id` (`mapping_set_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -775,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -790,17 +781,16 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
- KEY `transcript_idx` (`transcript_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -812,12 +802,12 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -833,23 +823,22 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
- KEY `translation_idx` (`translation_id`),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -858,31 +847,30 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
- KEY `id_idx` (`identifier`(50)),
- KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
-) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1000007 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/test_collection/core/table.sql b/modules/t/test-genome-DBs/test_collection/core/table.sql
index 35a127b25a2eca719dea59d1a11fe62877af60f8..ebd656a1dea92d65fd65d4b118d9116e61aeca66 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -19,66 +19,67 @@ CREATE TABLE `alt_allele_group` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
- `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(128) NOT NULL,
+ `logic_name` varchar(40) NOT NULL DEFAULT '',
`db` varchar(120) DEFAULT NULL,
`db_version` varchar(40) DEFAULT NULL,
`db_file` varchar(120) DEFAULT NULL,
`program` varchar(80) DEFAULT NULL,
`program_version` varchar(40) DEFAULT NULL,
`program_file` varchar(80) DEFAULT NULL,
- `parameters` text,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) DEFAULT NULL,
`module_version` varchar(40) DEFAULT NULL,
`gff_source` varchar(40) DEFAULT NULL,
`gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=InnoDB AUTO_INCREMENT=39 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
- `exc_seq_region_id` int(10) unsigned NOT NULL,
- `exc_seq_region_start` int(10) unsigned NOT NULL,
- `exc_seq_region_end` int(10) unsigned NOT NULL,
- `ori` int(11) NOT NULL,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` varchar(128) DEFAULT NULL,
PRIMARY KEY (`associated_group_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -94,16 +95,16 @@ CREATE TABLE `associated_xref` (
KEY `associated_object_idx` (`object_xref_id`),
KEY `associated_idx` (`xref_id`),
KEY `associated_group_idx` (`associated_group_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB AUTO_INCREMENT=391 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -116,7 +117,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -131,29 +132,29 @@ CREATE TABLE `data_file` (
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
KEY `df_analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
- `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `density_type_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `density_value` float NOT NULL,
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
- `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `block_size` int(11) NOT NULL,
- `region_features` int(11) NOT NULL,
- `value_type` enum('sum','ratio') NOT NULL,
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -162,16 +163,16 @@ CREATE TABLE `dependent_xref` (
PRIMARY KEY (`object_xref_id`),
KEY `dependent` (`dependent_xref_id`),
KEY `master_idx` (`master_xref_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -181,49 +182,48 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` tinytext NOT NULL,
- `ditag_side` enum('F','L','R') NOT NULL,
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_idx` (`ditag_id`),
- KEY `ditag_pair_idx` (`ditag_pair_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `hit_start` int(11) NOT NULL,
- `hit_end` int(11) NOT NULL,
- `hit_strand` tinyint(1) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text,
+ `external_data` text COLLATE latin1_bin,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -242,38 +242,37 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL,
- `transcript_id` int(10) unsigned NOT NULL,
- `rank` int(10) NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `db_name` varchar(100) NOT NULL,
- `db_release` varchar(255) DEFAULT NULL,
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
- `priority` int(11) NOT NULL,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) NOT NULL DEFAULT '',
+ `db_release` varchar(40) NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL','IGNORE','ALT_GENE') DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL,
- `description` text,
- PRIMARY KEY (`external_db_id`),
- UNIQUE KEY `db_name_idx` (`db_name`,`db_release`)
-) ENGINE=InnoDB AUTO_INCREMENT=50745 DEFAULT CHARSET=latin1;
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL,
- `synonym` varchar(100) NOT NULL,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -285,7 +284,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -297,24 +296,22 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`),
- KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
+ `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -322,9 +319,8 @@ CREATE TABLE `gene_attrib` (
`value` text NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `gene_idx` (`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -339,25 +335,25 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) NOT NULL,
- `id` varchar(40) NOT NULL,
- UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
- KEY `id_idx` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ `interpro_ac` varchar(40) NOT NULL DEFAULT '',
+ `id` varchar(40) NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -373,27 +369,27 @@ CREATE TABLE `intron_supporting_evidence` (
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) DEFAULT NULL,
`stain` varchar(40) DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
+ `map_name` varchar(30) NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
`new_db_name` varchar(80) NOT NULL DEFAULT '',
`old_release` varchar(5) NOT NULL DEFAULT '',
@@ -401,9 +397,8 @@ CREATE TABLE `mapping_session` (
`old_assembly` varchar(20) NOT NULL DEFAULT '',
`new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
- `species_id` int(10) NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -411,72 +406,71 @@ CREATE TABLE `mapping_set` (
`external_schema_build` varchar(20) NOT NULL,
PRIMARY KEY (`mapping_set_id`),
UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `marker` (
`marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
+ `left_primer` varchar(100) NOT NULL DEFAULT '',
+ `right_primer` varchar(100) NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL,
- `map_id` int(10) unsigned NOT NULL,
- `chromosome_name` varchar(15) NOT NULL,
- `marker_synonym_id` int(10) unsigned NOT NULL,
- `position` varchar(15) NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) DEFAULT NULL,
- `name` varchar(50) DEFAULT NULL,
+ `name` varchar(30) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) DEFAULT 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=InnoDB AUTO_INCREMENT=192 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
+ `table_name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -484,9 +478,8 @@ CREATE TABLE `misc_attrib` (
`value` text NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -496,46 +489,45 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`description` text NOT NULL,
- `max_length` int(10) unsigned NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
- `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`object_xref_id`),
- UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
- KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1;
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source_xref_id` int(10) unsigned DEFAULT NULL,
`linkage_type` varchar(3) DEFAULT NULL,
- UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `source_idx` (`source_xref_id`),
- KEY `object_idx` (`object_xref_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
`operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -553,7 +545,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -572,66 +564,66 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
`gene_id` int(10) unsigned DEFAULT NULL,
KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
`peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL,
- `exon_rank` smallint(5) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `start_phase` tinyint(4) NOT NULL,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `transcript_idx` (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(4) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -639,68 +631,68 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(10) unsigned NOT NULL,
- `seq_start` int(10) NOT NULL,
- `seq_end` int(10) NOT NULL,
- `hit_start` int(10) NOT NULL,
- `hit_end` int(10) NOT NULL,
- `hit_name` varchar(40) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `score` double DEFAULT NULL,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text,
- `hit_description` text,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
- KEY `translation_idx` (`translation_id`),
- KEY `hitname_idx` (`hit_name`),
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) NOT NULL,
- `repeat_class` varchar(100) NOT NULL,
- `repeat_type` varchar(40) NOT NULL,
- `repeat_consensus` text,
+ `repeat_name` varchar(255) NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL,
- `repeat_end` int(10) NOT NULL,
- `repeat_consensus_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
+ `name` varchar(40) NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=14 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -708,62 +700,60 @@ CREATE TABLE `seq_region_attrib` (
`value` text NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
- KEY `mapping_set_idx` (`mapping_set_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `mapping_set_id` (`mapping_set_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(250) NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
+ UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(1) NOT NULL,
- `display_label` varchar(255) NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=InnoDB AUTO_INCREMENT=37 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') NOT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -776,7 +766,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -791,7 +781,7 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -799,9 +789,8 @@ CREATE TABLE `transcript_attrib` (
`value` text NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -810,15 +799,15 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
`next_exon_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
- `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -834,7 +823,7 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=InnoDB AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -842,15 +831,14 @@ CREATE TABLE `translation_attrib` (
`value` text NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
KEY `translation_idx` (`translation_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- `external_db_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
`identifier` varchar(255) NOT NULL,
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
@@ -859,31 +847,30 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
`parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
- KEY `id_idx` (`identifier`(50)),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
- KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) NOT NULL,
`dbprimary_acc` varchar(512) NOT NULL,
`display_label` varchar(512) NOT NULL,
`version` varchar(10) DEFAULT NULL,
- `description` text,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=InnoDB AUTO_INCREMENT=91703 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;