diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 0b6bfa72296ef0f184bcbd14f568781f48de78b7..91ddc72f33138aff7d2874871894d33a3a0a0367 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -1,4 +1,4 @@
-1 \N schema_version 68
+1 \N schema_version 70
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
@@ -22,4 +22,11 @@
64 1 assembly.mapping chromosome:NCBI33#chunk
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
-67 1 species.production_name homo_sapiens
+67 1 species.production_name circ
+75 \N schema_type core
+76 \N patch patch_68_69_a.sql|schema_version
+77 \N patch patch_69_70_a.sql|schema_version
+78 \N patch patch_69_70_b.sql|add_mapping_set_history
+79 \N patch patch_69_70_c.sql|column_datatype_consistency
+80 \N patch patch_69_70_d.sql|data_file_id_auto_increment
+81 \N patch patch_69_70_e.sql|protein_feature_hit_description
diff --git a/modules/t/test-genome-DBs/circ/core/oligo_array.txt b/modules/t/test-genome-DBs/circ/core/oligo_array.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/modules/t/test-genome-DBs/circ/core/oligo_feature.txt b/modules/t/test-genome-DBs/circ/core/oligo_feature.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/modules/t/test-genome-DBs/circ/core/oligo_probe.txt b/modules/t/test-genome-DBs/circ/core/oligo_probe.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index 5470d191c3366e09fc3e7620b7c657c96ab9b713..1bd46b2f2a2e41fe6eb1adc3a930af0c5e76a70a 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -4,36 +4,36 @@ CREATE TABLE `alt_allele` (
`is_ref` tinyint(1) NOT NULL DEFAULT '0',
UNIQUE KEY `gene_idx` (`gene_id`),
UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=2 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,
- `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,
+ `logic_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `db` varchar(120) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `db_version` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `db_file` varchar(120) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `program` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `program_version` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `program_file` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text CHARACTER SET latin1 COLLATE latin1_bin,
+ `module` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `module_version` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `gff_source` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `gff_feature` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name` (`logic_name`),
KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1;
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,
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
+ `display_label` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text COLLATE latin1_bin,
+ `web_data` text CHARACTER SET latin1 COLLATE latin1_bin,
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `assembly` (
`asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -46,14 +46,14 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`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') CHARACTER SET latin1 COLLATE latin1_bin 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',
@@ -61,16 +61,16 @@ 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;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `code` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin,
+ `code` varchar(15) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=20 DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -83,12 +83,12 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
- `data_file_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
- `coord_system_id` int(11) NOT NULL,
- `analysis_id` int(11) NOT NULL,
+ `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
@@ -98,7 +98,7 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -110,17 +110,26 @@ 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;
+) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `dependent_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL,
+ `master_xref_id` int(10) unsigned NOT NULL,
+ `dependent_xref_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`object_xref_id`),
+ KEY `dependent` (`dependent_xref_id`),
+ KEY `master_idx` (`master_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
@@ -129,7 +138,7 @@ CREATE TABLE `ditag` (
`tag_count` smallint(6) DEFAULT '1',
`sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -148,13 +157,13 @@ CREATE TABLE `ditag_feature` (
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=4828763 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 CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -165,15 +174,15 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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 COLLATE latin1_bin,
+ `cigar_line` text CHARACTER SET latin1 COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text COLLATE latin1_bin,
+ `external_data` text CHARACTER SET latin1 COLLATE latin1_bin,
`pair_dna_align_feature_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -182,14 +191,14 @@ CREATE TABLE `dna_align_feature` (
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`),
KEY `pair_idx` (`pair_dna_align_feature_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=29797140 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `dnac` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumblob NOT NULL,
- `n_line` text COLLATE latin1_bin,
+ `n_line` text CHARACTER SET latin1 COLLATE latin1_bin,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -208,7 +217,7 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=162034 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -217,28 +226,28 @@ CREATE TABLE `exon_transcript` (
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `db_release` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') CHARACTER SET latin1 COLLATE latin1_bin 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,
- `description` text COLLATE latin1_bin,
+ `db_display_name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `secondary_db_name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `secondary_db_table` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -264,29 +273,29 @@ CREATE TABLE `gene` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=18276 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `gene_stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `gene_idx` (`gene_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -296,18 +305,18 @@ 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 COLLATE latin1_bin,
+ `cigar_line` text CHARACTER SET latin1 COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `id` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
KEY `id` (`id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -322,55 +331,56 @@ CREATE TABLE `intron_supporting_evidence` (
`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;
+) 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 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 NOT NULL DEFAULT '',
- `stain` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `band` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `stain` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_db_name` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_release` varchar(5) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_release` varchar(5) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_assembly` varchar(20) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
- `schema_build` varchar(20) NOT NULL,
- PRIMARY KEY (`schema_build`)
-) ENGINE=MyISAM;
+ `internal_schema_build` varchar(20) NOT NULL,
+ `external_schema_build` varchar(20) NOT NULL,
+ UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
+) 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) COLLATE latin1_bin NOT NULL DEFAULT '',
- `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `left_primer` varchar(100) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `right_primer` varchar(100) CHARACTER SET latin1 COLLATE latin1_bin 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') CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -383,28 +393,28 @@ 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;
+) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `name` varchar(30) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -414,22 +424,22 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=82 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `table_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -439,71 +449,36 @@ 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;
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
`max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
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') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
- `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `xref_id` int(10) unsigned NOT NULL,
+ `linkage_annotation` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin 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;
-
-CREATE TABLE `oligo_array` (
- `oligo_array_id` int(11) NOT NULL AUTO_INCREMENT,
- `parent_array_id` int(11) DEFAULT NULL,
- `probe_setsize` tinyint(4) NOT NULL DEFAULT '0',
- `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `type` enum('AFFY','OLIGO') COLLATE latin1_bin DEFAULT NULL,
- PRIMARY KEY (`oligo_array_id`)
-) ENGINE=MyISAM;
-
-CREATE TABLE `oligo_feature` (
- `oligo_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(11) NOT NULL DEFAULT '0',
- `seq_region_end` int(11) NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
- `mismatches` tinyint(4) DEFAULT NULL,
- `oligo_probe_id` int(11) NOT NULL DEFAULT '0',
- `analysis_id` int(11) NOT NULL DEFAULT '0',
- PRIMARY KEY (`oligo_feature_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
- KEY `probe_idx` (`oligo_probe_id`)
-) ENGINE=MyISAM;
-
-CREATE TABLE `oligo_probe` (
- `oligo_probe_id` int(11) NOT NULL AUTO_INCREMENT,
- `oligo_array_id` int(11) NOT NULL DEFAULT '0',
- `probeset` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `name` varchar(20) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin,
- `length` smallint(5) NOT NULL DEFAULT '0',
- PRIMARY KEY (`oligo_probe_id`,`oligo_array_id`),
- KEY `probeset_idx` (`probeset`),
- KEY `array_idx` (`oligo_array_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=253685 DEFAULT CHARSET=latin1;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -512,7 +487,7 @@ CREATE TABLE `ontology_xref` (
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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
`operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -530,7 +505,7 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -549,21 +524,21 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=3 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=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `peptide_seq` mediumtext CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -579,7 +554,7 @@ 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;
+) ENGINE=MyISAM AUTO_INCREMENT=192 DEFAULT CHARSET=latin1;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -588,11 +563,11 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=18084 DEFAULT CHARSET=latin1;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -602,12 +577,12 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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 COLLATE latin1_bin,
+ `cigar_line` text CHARACTER SET latin1 COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
@@ -616,7 +591,7 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=11554505 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -625,27 +600,29 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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,
PRIMARY KEY (`protein_feature_id`),
KEY `translation_id` (`translation_id`),
KEY `hitname_index` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=242847 DEFAULT CHARSET=latin1;
CREATE TABLE `qtl` (
`qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `trait` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `trait` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` float DEFAULT NULL,
`flank_marker_id_1` int(11) DEFAULT NULL,
`flank_marker_id_2` int(11) DEFAULT NULL,
`peak_marker_id` int(11) DEFAULT NULL,
PRIMARY KEY (`qtl_id`),
KEY `trait_idx` (`trait`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `qtl_feature` (
`seq_region_id` int(11) NOT NULL DEFAULT '0',
@@ -656,29 +633,29 @@ CREATE TABLE `qtl_feature` (
KEY `qtl_id` (`qtl_id`),
KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `qtl_synonym` (
`qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`qtl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source_database` enum('rat genome database','ratmap') COLLATE latin1_bin NOT NULL DEFAULT 'rat genome database',
- `source_primary_id` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `source_database` enum('rat genome database','ratmap') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'rat genome database',
+ `source_primary_id` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`qtl_synonym_id`),
KEY `qtl_idx` (`qtl_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
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_consensus` text COLLATE latin1_bin,
+ `repeat_name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_consensus` text CHARACTER SET latin1 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;
+) ENGINE=MyISAM AUTO_INCREMENT=1018 DEFAULT CHARSET=latin1;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -695,32 +672,32 @@ 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 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=922515 DEFAULT CHARSET=latin1 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) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1;
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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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_id` (`mapping_set_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -729,7 +706,7 @@ CREATE TABLE `seq_region_synonym` (
`external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -737,35 +714,35 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
- `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `new_stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin 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') CHARACTER SET latin1 COLLATE latin1_bin 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`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin 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`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -792,15 +769,15 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=21741 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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -808,15 +785,15 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
`previous_exon_id` int(10) unsigned NOT NULL,
`next_exon_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin 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`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -832,15 +809,15 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=21741 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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `translation_idx` (`translation_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `unconventional_transcript_association` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -848,43 +825,43 @@ CREATE TABLE `unconventional_transcript_association` (
`interaction_type` enum('antisense','sense_intronic','sense_overlaping_exonic','chimeric_sense_exonic') DEFAULT NULL,
KEY `transcript_id` (`transcript_id`),
KEY `gene_id` (`gene_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
`unmapped_reason_id` smallint(5) 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',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') CHARACTER SET latin1 COLLATE latin1_bin DEFAULT 'RawContig',
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;
+) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` smallint(5) 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `full_description` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`external_db_id` int(11) NOT NULL DEFAULT '0',
- `dbprimary_acc` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `display_label` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `version` varchar(10) COLLATE latin1_bin NOT NULL DEFAULT '',
- `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 '',
+ `dbprimary_acc` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `display_label` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `version` varchar(10) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+ `info_text` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM AUTO_INCREMENT=1000000 DEFAULT CHARSET=latin1;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 171aa68d0b92089ebf0a689caf00a89d30071516..fa89bb33a40a2f9335abca54422a37ab57b16702 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -29,3 +29,4 @@
74 \N patch patch_69_70_c.sql|column_datatype_consistency
75 \N patch patch_69_70_d.sql|data_file_id_auto_increment
76 \N patch patch_69_70_e.sql|protein_feature_hit_description
+77 \N schema_type core
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.sql b/modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.sql
deleted file mode 100644
index 4090bb01255d3d8fd1f1eec693c062ecda80074f..0000000000000000000000000000000000000000
--- a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.sql
+++ /dev/null
@@ -1,41 +0,0 @@
--- MySQL dump 10.13 Distrib 5.1.61, for redhat-linux-gnu (x86_64)
---
--- Host: mysql-eg-devel-1.ebi.ac.uk Database: homo_sapiens_core_test_db
--- ------------------------------------------------------
--- Server version 5.1.49-log
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
-/*!40103 SET TIME_ZONE='+00:00' */;
-/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
-/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
-
---
--- Table structure for table `oligo_array`
---
-
-DROP TABLE IF EXISTS `oligo_array`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `oligo_array` (
- `oligo_array_id` int(11) NOT NULL AUTO_INCREMENT,
- `parent_array_id` int(11) DEFAULT NULL,
- `probe_setsize` tinyint(4) NOT NULL DEFAULT '0',
- `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `type` enum('AFFY','OLIGO') COLLATE latin1_bin DEFAULT NULL,
- PRIMARY KEY (`oligo_array_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
-/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
-
-/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
-/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-
--- Dump completed on 2012-11-05 10:52:11
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.txt b/modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.sql b/modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.sql
deleted file mode 100644
index 2e0396c43eff863584dd663fa935f396fbbbcf10..0000000000000000000000000000000000000000
--- a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.sql
+++ /dev/null
@@ -1,46 +0,0 @@
--- MySQL dump 10.13 Distrib 5.1.61, for redhat-linux-gnu (x86_64)
---
--- Host: mysql-eg-devel-1.ebi.ac.uk Database: homo_sapiens_core_test_db
--- ------------------------------------------------------
--- Server version 5.1.49-log
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
-/*!40103 SET TIME_ZONE='+00:00' */;
-/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
-/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
-
---
--- Table structure for table `oligo_feature`
---
-
-DROP TABLE IF EXISTS `oligo_feature`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `oligo_feature` (
- `oligo_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(11) NOT NULL DEFAULT '0',
- `seq_region_end` int(11) NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
- `mismatches` tinyint(4) DEFAULT NULL,
- `oligo_probe_id` int(11) NOT NULL DEFAULT '0',
- `analysis_id` int(11) NOT NULL DEFAULT '0',
- PRIMARY KEY (`oligo_feature_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
- KEY `probe_idx` (`oligo_probe_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
-/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
-
-/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
-/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-
--- Dump completed on 2012-11-05 10:52:11
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql b/modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql
deleted file mode 100644
index 124e286be4ca73ef77fa48a1e42c53a19f1f91a6..0000000000000000000000000000000000000000
--- a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql
+++ /dev/null
@@ -1,44 +0,0 @@
--- MySQL dump 10.13 Distrib 5.1.61, for redhat-linux-gnu (x86_64)
---
--- Host: mysql-eg-devel-1.ebi.ac.uk Database: homo_sapiens_core_test_db
--- ------------------------------------------------------
--- Server version 5.1.49-log
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
-/*!40103 SET TIME_ZONE='+00:00' */;
-/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
-/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
-
---
--- Table structure for table `oligo_probe`
---
-
-DROP TABLE IF EXISTS `oligo_probe`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `oligo_probe` (
- `oligo_probe_id` int(11) NOT NULL AUTO_INCREMENT,
- `oligo_array_id` int(11) NOT NULL DEFAULT '0',
- `probeset` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `name` varchar(20) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin,
- `length` smallint(5) NOT NULL DEFAULT '0',
- PRIMARY KEY (`oligo_probe_id`,`oligo_array_id`),
- KEY `probeset_idx` (`probeset`),
- KEY `array_idx` (`oligo_array_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
-/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
-
-/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
-/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-
--- Dump completed on 2012-11-05 10:52:11
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.txt b/modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql b/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql
index d63b0c329946531f7854d44f66e51c2f7d15c51d..114e733886d7aefd39a640f4a55aa7a46e1c1010 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql
@@ -32,6 +32,7 @@ CREATE TABLE `protein_feature` (
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
`hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
KEY `translation_id` (`translation_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
index 8f98a7fe0a90b11c243b54e923482c18b1a23140..3170fb2f3ebf4bebbb0969d47ddcb7b719da6d6f 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
@@ -1,156 +1,156 @@
-27374 21716 76 99 45 75 0 41 0 0 0 \N
-217249 21716 47 151 49 79 PF000001 41 87.1 8.2e-25 0 \N
-242732 21716 80 160 71 101 0 41 0 3.2e-11 0 \N
-217179 21717 1 94 49 79 PF000019 41 99.1 3.3e-28 0 \N
-242734 21717 3 91 71 101 0 41 0 1.7e-15 0 \N
-217309 21718 76 201 49 79 PF000019 41 118.9 8.9e-34 0 \N
-242735 21718 1 185 71 101 0 41 0 3e-14 0 \N
-27378 21719 90 117 45 75 0 41 0 0 0 \N
-83043 21719 21 41 44 74 0 41 2.37 0 0 \N
-242736 21719 76 124 71 101 0 41 0 0.0017 0 \N
-24545 21720 79 101 46 76 0 41 0 0 0 \N
-24546 21720 106 123 46 76 0 41 0 0 0 \N
-24547 21720 138 155 46 76 0 41 0 0 0 \N
-24548 21720 192 214 46 76 0 41 0 0 0 \N
-83044 21720 37 59 44 74 0 41 2.67 0 0 \N
-116148 21720 93 100 42 72 0 41 0 0 0 \N
-83051 21721 24 37 44 74 0 41 2.3 0 0 \N
-83052 21721 170 184 44 74 0 41 1.97 0 0 \N
-83053 21721 212 235 44 74 0 41 2.47 0 0 \N
-242779 21721 47 146 71 101 0 41 0 0.002 0 \N
-83045 21722 135 149 44 74 0 41 1.97 0 0 \N
-83046 21722 171 187 44 74 PF000001 41 1.66 0 0 \N
-83047 21722 217 230 44 74 0 41 1.09 0 0 \N
-83048 21722 361 376 44 74 0 41 2.44 0 0 \N
-83049 21722 470 482 44 74 0 41 2.2 0 0 \N
-83050 21722 512 520 44 74 0 41 0.76 0 0 \N
-116149 21722 347 358 42 72 0 41 0 0 0 \N
-116150 21723 268 290 42 72 0 41 1 0 0 \N
-116151 21723 377 389 42 72 0 41 1 0 0 \N
-130095 21723 144 241 41 71 0 41 26.88 0 0 \N
-130097 21723 78 138 41 71 0 41 19.623 0 0 \N
-161506 21723 144 158 40 70 0 41 394 9.81e-06 0 \N
-161508 21723 165 175 40 70 0 41 321 2.59e-05 0 \N
-161510 21723 177 188 40 70 0 41 288 1.03e-06 0 \N
-161512 21723 194 204 40 70 0 41 295 4.86e-05 0 \N
-161514 21723 215 229 40 70 0 41 349 7e-07 0 \N
-161516 21723 81 91 40 70 0 41 266 3.18e-05 0 \N
-161518 21723 95 110 40 70 0 41 334 1.38e-07 0 \N
-161520 21723 111 120 40 70 0 41 225 0.0222 0 \N
-161522 21723 124 136 40 70 0 41 341 1.82e-06 0 \N
-161524 21723 83 103 40 70 0 41 565 7.11e-09 0 \N
-161526 21723 103 119 40 70 0 41 188 0.099 0 \N
-217502 21723 83 138 49 79 58 41 98.9 6.4e-27 0 \N
-217503 21723 146 228 49 79 79 41 150.9 1.5e-42 0 \N
-217504 21723 264 513 49 79 294 41 260.8 1.2e-75 0 \N
-242780 21723 244 526 71 101 0 41 0 2.3e-79 0 \N
-242781 21723 138 282 71 101 0 41 0 1.3e-33 0 \N
-242782 21723 81 162 71 101 0 41 0 2.5e-22 0 \N
-24549 21724 263 285 46 76 0 41 0 0 0 \N
-24550 21724 329 351 46 76 0 41 0 0 0 \N
-24551 21724 361 383 46 76 0 41 0 0 0 \N
-24552 21724 396 418 46 76 0 41 0 0 0 \N
-24553 21724 433 455 46 76 0 41 0 0 0 \N
-24554 21724 483 505 46 76 0 41 0 0 0 \N
-24555 21724 515 537 46 76 0 41 0 0 0 \N
-24556 21724 550 572 46 76 0 41 0 0 0 \N
-24557 21724 587 609 46 76 0 41 0 0 0 \N
-83054 21724 270 275 44 74 0 41 0.92 0 0 \N
-83055 21724 326 335 44 74 0 41 1.97 0 0 \N
-83056 21724 367 378 44 74 0 41 2.05 0 0 \N
-83057 21724 513 529 44 74 0 41 2.42 0 0 \N
-217569 21724 37 583 49 79 600 41 1244.7 0 0 \N
-242783 21724 3 576 71 101 0 41 0 0.0058 0 \N
-27431 21725 113 133 45 75 0 41 0 0 0 \N
-83058 21725 30 40 44 74 0 41 1.87 0 0 \N
-83059 21725 109 135 44 74 0 41 2.49 0 0 \N
-217397 21725 146 331 49 79 324 41 84.5 1.4e-22 0 \N
-83060 21726 369 397 44 74 0 41 2.53 0 0 \N
-83061 21726 417 432 44 74 0 41 2.3 0 0 \N
-83062 21726 443 458 44 74 0 41 2.43 0 0 \N
-116152 21726 70 92 42 72 0 41 1 0 0 \N
-116153 21726 100 120 42 72 0 41 1 0 0 \N
-116154 21726 129 149 42 72 0 41 1 0 0 \N
-116155 21726 158 178 42 72 0 41 1 0 0 \N
-116156 21726 193 213 42 72 0 41 0 0 0 \N
-116157 21726 221 242 42 72 0 41 1 0 0 \N
-130099 21726 68 97 41 71 0 41 14.815 0 0 \N
-130101 21726 98 125 41 71 0 41 11.676 0 0 \N
-130103 21726 127 154 41 71 0 41 9.556 0 0 \N
-130105 21726 156 183 41 71 0 41 9.536 0 0 \N
-130107 21726 191 218 41 71 0 41 12.092 0 0 \N
-130109 21726 219 247 41 71 0 41 11.281 0 0 \N
-217476 21726 68 94 49 79 24 41 12.8 0.29 0 \N
-217477 21726 100 122 49 79 24 41 25.3 9.2e-05 0 \N
-217478 21726 129 151 49 79 24 41 19.7 0.0045 0 \N
-217479 21726 158 180 49 79 24 41 19.2 0.0063 0 \N
-217480 21726 193 215 49 79 24 41 22.9 0.00049 0 \N
-217481 21726 221 244 49 79 24 41 24 0.00023 0 \N
-242784 21726 80 124 71 101 0 41 0 1.5e-09 0 \N
-242785 21726 205 245 71 101 0 41 0 7.5e-09 0 \N
-242786 21726 58 85 71 101 0 41 0 0.0011 0 \N
-34517 21727 1 26 43 73 0 41 0 0 0 \N
-83063 21727 15 22 44 74 0 41 0.81 0 0 \N
-34518 21728 1 26 43 73 0 41 0 0 0 \N
-83064 21728 15 22 44 74 0 41 0.81 0 0 \N
-27435 21729 355 375 45 75 0 41 0 0 0 \N
-27437 21729 436 473 45 75 0 41 0 0 0 \N
-27440 21729 482 519 45 75 0 41 0 0 0 \N
-27443 21729 541 579 45 75 0 41 0 0 0 \N
-83065 21729 6 17 44 74 0 41 2.13 0 0 \N
-83066 21729 370 407 44 74 0 41 2.15 0 0 \N
-83067 21729 437 458 44 74 0 41 2.44 0 0 \N
-83068 21729 493 514 44 74 0 41 2.5 0 0 \N
-83069 21729 537 548 44 74 0 41 1.9 0 0 \N
-83070 21729 685 697 44 74 0 41 2.26 0 0 \N
-83071 21729 711 735 44 74 0 41 2.42 0 0 \N
-116158 21729 96 103 42 72 0 41 0 0 0 \N
-116159 21729 239 250 42 72 0 41 1 0 0 \N
-130111 21729 6 256 41 71 0 41 55.446 0 0 \N
-161528 21729 87 108 40 70 0 41 911 4.44e-16 0 \N
-161530 21729 206 223 40 70 0 41 585 2.63e-10 0 \N
-161532 21729 240 258 40 70 0 41 576 8.36e-12 0 \N
-161534 21729 290 311 40 70 0 41 833 4.44e-16 0 \N
-217672 21729 55 341 49 79 373 41 576.3 1.3e-170 0 \N
-242791 21729 4 365 71 101 0 41 0 8.4e-131 0 \N
-83072 21730 3 16 44 74 0 41 1.78 0 0 \N
-83073 21730 140 153 44 74 0 41 2.15 0 0 \N
-83074 21730 442 469 44 74 0 41 1.89 0 0 \N
-83075 21730 644 654 44 74 0 41 1.87 0 0 \N
-83076 21730 1221 1235 44 74 0 41 2.15 0 0 \N
-83077 21730 1250 1264 44 74 0 41 2.2 0 0 \N
-83078 21731 194 211 44 74 0 41 1.95 0 0 \N
-83079 21731 335 348 44 74 0 41 2.15 0 0 \N
-83080 21731 637 664 44 74 0 41 1.89 0 0 \N
-83081 21731 839 849 44 74 0 41 1.87 0 0 \N
-83082 21732 33 61 44 74 0 41 2.68 0 0 \N
-83083 21732 161 178 44 74 0 41 1.83 0 0 \N
-83084 21732 375 396 44 74 0 41 1.93 0 0 \N
-116160 21732 92 102 42 72 0 41 0 0 0 \N
-130113 21732 235 252 41 71 0 41 3 0 0 \N
-83085 21735 76 95 44 74 0 41 2.54 0 0 \N
-83086 21735 104 122 44 74 0 41 2.65 0 0 \N
-83087 21736 5 20 44 74 0 41 1.92 0 0 \N
-83088 21737 47 65 44 74 0 41 2.35 0 0 \N
-83089 21737 72 83 44 74 0 41 1.65 0 0 \N
-83090 21737 110 125 44 74 0 41 2.42 0 0 \N
-83091 21737 142 154 44 74 0 41 2.16 0 0 \N
-83092 21737 166 177 44 74 0 41 2.08 0 0 \N
-83093 21737 565 576 44 74 0 41 1.96 0 0 \N
-116161 21737 309 316 42 72 0 41 0 0 0 \N
-116162 21737 643 655 42 72 0 41 0 0 0 \N
-217810 21737 223 296 49 79 87 41 121 1.5e-33 0 \N
-217811 21737 576 849 49 79 418 41 -74 8.5e-06 0 \N
-242841 21737 573 848 71 101 0 41 0 3e-50 0 \N
-242842 21737 216 351 71 101 0 41 0 1.2e-41 0 \N
-27455 21738 193 213 45 75 0 41 0 0 0 \N
-83094 21738 256 267 44 74 0 41 2.12 0 0 \N
-130115 21738 14 116 41 71 0 41 8.924 0 0 \N
-217326 21738 15 117 49 79 106 41 28 1.5e-05 0 \N
-217327 21738 210 257 49 79 56 41 106 4.7e-29 0 \N
-242845 21738 13 115 71 101 0 41 0 3e-17 0 \N
-83095 21739 44 56 44 74 0 41 2.19 0 0 \N
-130117 21739 144 201 41 71 0 41 9.695 0 0 \N
-217297 21739 141 168 49 79 29 41 4.4 1.7 0 \N
-217298 21739 176 204 49 79 29 41 12.7 0.15 0 \N
-242846 21739 117 207 71 101 0 41 0 4e-10 0 \N
+27374 21716 76 99 45 75 0 41 0 0 0 \N \N
+217249 21716 47 151 49 79 PF000001 41 87.1 8.2e-25 0 \N \N
+242732 21716 80 160 71 101 0 41 0 3.2e-11 0 \N \N
+217179 21717 1 94 49 79 PF000019 41 99.1 3.3e-28 0 \N \N
+242734 21717 3 91 71 101 0 41 0 1.7e-15 0 \N \N
+217309 21718 76 201 49 79 PF000019 41 118.9 8.9e-34 0 \N \N
+242735 21718 1 185 71 101 0 41 0 3e-14 0 \N \N
+27378 21719 90 117 45 75 0 41 0 0 0 \N \N
+83043 21719 21 41 44 74 0 41 2.37 0 0 \N \N
+242736 21719 76 124 71 101 0 41 0 0.0017 0 \N \N
+24545 21720 79 101 46 76 0 41 0 0 0 \N \N
+24546 21720 106 123 46 76 0 41 0 0 0 \N \N
+24547 21720 138 155 46 76 0 41 0 0 0 \N \N
+24548 21720 192 214 46 76 0 41 0 0 0 \N \N
+83044 21720 37 59 44 74 0 41 2.67 0 0 \N \N
+116148 21720 93 100 42 72 0 41 0 0 0 \N \N
+83051 21721 24 37 44 74 0 41 2.3 0 0 \N \N
+83052 21721 170 184 44 74 0 41 1.97 0 0 \N \N
+83053 21721 212 235 44 74 0 41 2.47 0 0 \N \N
+242779 21721 47 146 71 101 0 41 0 0.002 0 \N \N
+83045 21722 135 149 44 74 0 41 1.97 0 0 \N \N
+83046 21722 171 187 44 74 PF000001 41 1.66 0 0 \N \N
+83047 21722 217 230 44 74 0 41 1.09 0 0 \N \N
+83048 21722 361 376 44 74 0 41 2.44 0 0 \N \N
+83049 21722 470 482 44 74 0 41 2.2 0 0 \N \N
+83050 21722 512 520 44 74 0 41 0.76 0 0 \N \N
+116149 21722 347 358 42 72 0 41 0 0 0 \N \N
+116150 21723 268 290 42 72 0 41 1 0 0 \N \N
+116151 21723 377 389 42 72 0 41 1 0 0 \N \N
+130095 21723 144 241 41 71 0 41 26.88 0 0 \N \N
+130097 21723 78 138 41 71 0 41 19.623 0 0 \N \N
+161506 21723 144 158 40 70 0 41 394 9.81e-06 0 \N \N
+161508 21723 165 175 40 70 0 41 321 2.59e-05 0 \N \N
+161510 21723 177 188 40 70 0 41 288 1.03e-06 0 \N \N
+161512 21723 194 204 40 70 0 41 295 4.86e-05 0 \N \N
+161514 21723 215 229 40 70 0 41 349 7e-07 0 \N \N
+161516 21723 81 91 40 70 0 41 266 3.18e-05 0 \N \N
+161518 21723 95 110 40 70 0 41 334 1.38e-07 0 \N \N
+161520 21723 111 120 40 70 0 41 225 0.0222 0 \N \N
+161522 21723 124 136 40 70 0 41 341 1.82e-06 0 \N \N
+161524 21723 83 103 40 70 0 41 565 7.11e-09 0 \N \N
+161526 21723 103 119 40 70 0 41 188 0.099 0 \N \N
+217502 21723 83 138 49 79 58 41 98.9 6.4e-27 0 \N \N
+217503 21723 146 228 49 79 79 41 150.9 1.5e-42 0 \N \N
+217504 21723 264 513 49 79 294 41 260.8 1.2e-75 0 \N \N
+242780 21723 244 526 71 101 0 41 0 2.3e-79 0 \N \N
+242781 21723 138 282 71 101 0 41 0 1.3e-33 0 \N \N
+242782 21723 81 162 71 101 0 41 0 2.5e-22 0 \N \N
+24549 21724 263 285 46 76 0 41 0 0 0 \N \N
+24550 21724 329 351 46 76 0 41 0 0 0 \N \N
+24551 21724 361 383 46 76 0 41 0 0 0 \N \N
+24552 21724 396 418 46 76 0 41 0 0 0 \N \N
+24553 21724 433 455 46 76 0 41 0 0 0 \N \N
+24554 21724 483 505 46 76 0 41 0 0 0 \N \N
+24555 21724 515 537 46 76 0 41 0 0 0 \N \N
+24556 21724 550 572 46 76 0 41 0 0 0 \N \N
+24557 21724 587 609 46 76 0 41 0 0 0 \N \N
+83054 21724 270 275 44 74 0 41 0.92 0 0 \N \N
+83055 21724 326 335 44 74 0 41 1.97 0 0 \N \N
+83056 21724 367 378 44 74 0 41 2.05 0 0 \N \N
+83057 21724 513 529 44 74 0 41 2.42 0 0 \N \N
+217569 21724 37 583 49 79 600 41 1244.7 0 0 \N \N
+242783 21724 3 576 71 101 0 41 0 0.0058 0 \N \N
+27431 21725 113 133 45 75 0 41 0 0 0 \N \N
+83058 21725 30 40 44 74 0 41 1.87 0 0 \N \N
+83059 21725 109 135 44 74 0 41 2.49 0 0 \N \N
+217397 21725 146 331 49 79 324 41 84.5 1.4e-22 0 \N \N
+83060 21726 369 397 44 74 0 41 2.53 0 0 \N \N
+83061 21726 417 432 44 74 0 41 2.3 0 0 \N \N
+83062 21726 443 458 44 74 0 41 2.43 0 0 \N \N
+116152 21726 70 92 42 72 0 41 1 0 0 \N \N
+116153 21726 100 120 42 72 0 41 1 0 0 \N \N
+116154 21726 129 149 42 72 0 41 1 0 0 \N \N
+116155 21726 158 178 42 72 0 41 1 0 0 \N \N
+116156 21726 193 213 42 72 0 41 0 0 0 \N \N
+116157 21726 221 242 42 72 0 41 1 0 0 \N \N
+130099 21726 68 97 41 71 0 41 14.815 0 0 \N \N
+130101 21726 98 125 41 71 0 41 11.676 0 0 \N \N
+130103 21726 127 154 41 71 0 41 9.556 0 0 \N \N
+130105 21726 156 183 41 71 0 41 9.536 0 0 \N \N
+130107 21726 191 218 41 71 0 41 12.092 0 0 \N \N
+130109 21726 219 247 41 71 0 41 11.281 0 0 \N \N
+217476 21726 68 94 49 79 24 41 12.8 0.29 0 \N \N
+217477 21726 100 122 49 79 24 41 25.3 9.2e-05 0 \N \N
+217478 21726 129 151 49 79 24 41 19.7 0.0045 0 \N \N
+217479 21726 158 180 49 79 24 41 19.2 0.0063 0 \N \N
+217480 21726 193 215 49 79 24 41 22.9 0.00049 0 \N \N
+217481 21726 221 244 49 79 24 41 24 0.00023 0 \N \N
+242784 21726 80 124 71 101 0 41 0 1.5e-09 0 \N \N
+242785 21726 205 245 71 101 0 41 0 7.5e-09 0 \N \N
+242786 21726 58 85 71 101 0 41 0 0.0011 0 \N \N
+34517 21727 1 26 43 73 0 41 0 0 0 \N \N
+83063 21727 15 22 44 74 0 41 0.81 0 0 \N \N
+34518 21728 1 26 43 73 0 41 0 0 0 \N \N
+83064 21728 15 22 44 74 0 41 0.81 0 0 \N \N
+27435 21729 355 375 45 75 0 41 0 0 0 \N \N
+27437 21729 436 473 45 75 0 41 0 0 0 \N \N
+27440 21729 482 519 45 75 0 41 0 0 0 \N \N
+27443 21729 541 579 45 75 0 41 0 0 0 \N \N
+83065 21729 6 17 44 74 0 41 2.13 0 0 \N \N
+83066 21729 370 407 44 74 0 41 2.15 0 0 \N \N
+83067 21729 437 458 44 74 0 41 2.44 0 0 \N \N
+83068 21729 493 514 44 74 0 41 2.5 0 0 \N \N
+83069 21729 537 548 44 74 0 41 1.9 0 0 \N \N
+83070 21729 685 697 44 74 0 41 2.26 0 0 \N \N
+83071 21729 711 735 44 74 0 41 2.42 0 0 \N \N
+116158 21729 96 103 42 72 0 41 0 0 0 \N \N
+116159 21729 239 250 42 72 0 41 1 0 0 \N \N
+130111 21729 6 256 41 71 0 41 55.446 0 0 \N \N
+161528 21729 87 108 40 70 0 41 911 4.44e-16 0 \N \N
+161530 21729 206 223 40 70 0 41 585 2.63e-10 0 \N \N
+161532 21729 240 258 40 70 0 41 576 8.36e-12 0 \N \N
+161534 21729 290 311 40 70 0 41 833 4.44e-16 0 \N \N
+217672 21729 55 341 49 79 373 41 576.3 1.3e-170 0 \N \N
+242791 21729 4 365 71 101 0 41 0 8.4e-131 0 \N \N
+83072 21730 3 16 44 74 0 41 1.78 0 0 \N \N
+83073 21730 140 153 44 74 0 41 2.15 0 0 \N \N
+83074 21730 442 469 44 74 0 41 1.89 0 0 \N \N
+83075 21730 644 654 44 74 0 41 1.87 0 0 \N \N
+83076 21730 1221 1235 44 74 0 41 2.15 0 0 \N \N
+83077 21730 1250 1264 44 74 0 41 2.2 0 0 \N \N
+83078 21731 194 211 44 74 0 41 1.95 0 0 \N \N
+83079 21731 335 348 44 74 0 41 2.15 0 0 \N \N
+83080 21731 637 664 44 74 0 41 1.89 0 0 \N \N
+83081 21731 839 849 44 74 0 41 1.87 0 0 \N \N
+83082 21732 33 61 44 74 0 41 2.68 0 0 \N \N
+83083 21732 161 178 44 74 0 41 1.83 0 0 \N \N
+83084 21732 375 396 44 74 0 41 1.93 0 0 \N \N
+116160 21732 92 102 42 72 0 41 0 0 0 \N \N
+130113 21732 235 252 41 71 0 41 3 0 0 \N \N
+83085 21735 76 95 44 74 0 41 2.54 0 0 \N \N
+83086 21735 104 122 44 74 0 41 2.65 0 0 \N \N
+83087 21736 5 20 44 74 0 41 1.92 0 0 \N \N
+83088 21737 47 65 44 74 0 41 2.35 0 0 \N \N
+83089 21737 72 83 44 74 0 41 1.65 0 0 \N \N
+83090 21737 110 125 44 74 0 41 2.42 0 0 \N \N
+83091 21737 142 154 44 74 0 41 2.16 0 0 \N \N
+83092 21737 166 177 44 74 0 41 2.08 0 0 \N \N
+83093 21737 565 576 44 74 0 41 1.96 0 0 \N \N
+116161 21737 309 316 42 72 0 41 0 0 0 \N \N
+116162 21737 643 655 42 72 0 41 0 0 0 \N \N
+217810 21737 223 296 49 79 87 41 121 1.5e-33 0 \N \N
+217811 21737 576 849 49 79 418 41 -74 8.5e-06 0 \N \N
+242841 21737 573 848 71 101 0 41 0 3e-50 0 \N \N
+242842 21737 216 351 71 101 0 41 0 1.2e-41 0 \N \N
+27455 21738 193 213 45 75 0 41 0 0 0 \N \N
+83094 21738 256 267 44 74 0 41 2.12 0 0 \N \N
+130115 21738 14 116 41 71 0 41 8.924 0 0 \N \N
+217326 21738 15 117 49 79 106 41 28 1.5e-05 0 \N \N
+217327 21738 210 257 49 79 56 41 106 4.7e-29 0 \N \N
+242845 21738 13 115 71 101 0 41 0 3e-17 0 \N \N
+83095 21739 44 56 44 74 0 41 2.19 0 0 \N \N
+130117 21739 144 201 41 71 0 41 9.695 0 0 \N \N
+217297 21739 141 168 49 79 29 41 4.4 1.7 0 \N \N
+217298 21739 176 204 49 79 29 41 12.7 0.15 0 \N \N
+242846 21739 117 207 71 101 0 41 0 4e-10 0 \N \N
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql b/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql
index f67b3ca394b7b8de957e2cc1a3084cfbd687214f..edfc78d69e761cd9f0659b71fcd8e37bcfe511ce 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql
@@ -31,6 +31,7 @@ CREATE TABLE `unmapped_object` (
`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,
PRIMARY KEY (`unmapped_object_id`),
KEY `id_idx` (`identifier`),
KEY `anal_idx` (`analysis_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt b/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt
index 8cf8d10b7fb98420fa08bf3cf80a2572226350cc..07ae8fa0008622c3129ad36f4d91d6fede75a603 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt
@@ -1,4 +1,4 @@
-1 xref 9 4100 X1234 1 70.5 60.2 21716 Translation
-2 xref 9 4100 X5678 1 75 50.1 21717 Transcript
-3 cDNA 1290 4200 cDNA12 2 80 40 21718 Translation
-4 cDNA 1290 4200 cDNA34 2 60.5 30.9 21719 Transcript
+1 xref 9 4100 X1234 1 70.5 60.2 21716 Translation \N
+2 xref 9 4100 X5678 1 75 50.1 21717 Transcript \N
+3 cDNA 1290 4200 cDNA12 2 80 40 21718 Translation \N
+4 cDNA 1290 4200 cDNA34 2 60.5 30.9 21719 Transcript \N
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 0b6bfa72296ef0f184bcbd14f568781f48de78b7..def9330c61309de5e6a915c76cc9ab4ecfd02575 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-1 \N schema_version 68
+1 \N schema_version 70
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
@@ -23,3 +23,10 @@
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
67 1 species.production_name homo_sapiens
+75 \N schema_type core
+76 \N patch patch_68_69_a.sql|schema_version
+77 \N patch patch_69_70_a.sql|schema_version
+78 \N patch patch_69_70_b.sql|add_mapping_set_history
+79 \N patch patch_69_70_c.sql|column_datatype_consistency
+80 \N patch patch_69_70_d.sql|data_file_id_auto_increment
+81 \N patch patch_69_70_e.sql|protein_feature_hit_description
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 5470d191c3366e09fc3e7620b7c657c96ab9b713..943536093635a14722bcdc58ad02b5d1ae682a92 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -4,36 +4,36 @@ CREATE TABLE `alt_allele` (
`is_ref` tinyint(1) NOT NULL DEFAULT '0',
UNIQUE KEY `gene_idx` (`gene_id`),
UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
-) ENGINE=MyISAM;
+) 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,
- `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,
+ `logic_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `db` varchar(120) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `db_version` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `db_file` varchar(120) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `program` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `program_version` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `program_file` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text CHARACTER SET latin1 COLLATE latin1_bin,
+ `module` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `module_version` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `gff_source` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `gff_feature` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name` (`logic_name`),
KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1;
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,
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
+ `display_label` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text COLLATE latin1_bin,
+ `web_data` text CHARACTER SET latin1 COLLATE latin1_bin,
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `assembly` (
`asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -46,14 +46,14 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`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') CHARACTER SET latin1 COLLATE latin1_bin 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',
@@ -61,16 +61,16 @@ 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;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `code` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin,
+ `code` varchar(15) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -83,12 +83,12 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
- `data_file_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
- `coord_system_id` int(11) NOT NULL,
- `analysis_id` int(11) NOT NULL,
+ `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
@@ -98,7 +98,7 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -110,17 +110,26 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `dependent_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL,
+ `master_xref_id` int(10) unsigned NOT NULL,
+ `dependent_xref_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`object_xref_id`),
+ KEY `dependent` (`dependent_xref_id`),
+ KEY `master_idx` (`master_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
@@ -129,7 +138,7 @@ CREATE TABLE `ditag` (
`tag_count` smallint(6) DEFAULT '1',
`sequence` text,
PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -148,13 +157,13 @@ CREATE TABLE `ditag_feature` (
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM ;
+) 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 CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -165,15 +174,15 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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 COLLATE latin1_bin,
+ `cigar_line` text CHARACTER SET latin1 COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text COLLATE latin1_bin,
+ `external_data` text CHARACTER SET latin1 COLLATE latin1_bin,
`pair_dna_align_feature_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -182,14 +191,14 @@ CREATE TABLE `dna_align_feature` (
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`),
KEY `pair_idx` (`pair_dna_align_feature_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `dnac` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumblob NOT NULL,
- `n_line` text COLLATE latin1_bin,
+ `n_line` text CHARACTER SET latin1 COLLATE latin1_bin,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -208,7 +217,7 @@ 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 ;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -217,28 +226,28 @@ CREATE TABLE `exon_transcript` (
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `db_release` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') CHARACTER SET latin1 COLLATE latin1_bin 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,
- `description` text COLLATE latin1_bin,
+ `db_display_name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `secondary_db_name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `secondary_db_table` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -264,29 +273,29 @@ CREATE TABLE `gene` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) 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) CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `gene_idx` (`gene_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -296,18 +305,18 @@ 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 COLLATE latin1_bin,
+ `cigar_line` text CHARACTER SET latin1 COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `id` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
KEY `id` (`id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -322,55 +331,56 @@ CREATE TABLE `intron_supporting_evidence` (
`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;
+) 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 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 NOT NULL DEFAULT '',
- `stain` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `band` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `stain` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_db_name` varchar(80) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_release` varchar(5) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_release` varchar(5) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_assembly` varchar(20) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
- `schema_build` varchar(20) NOT NULL,
- PRIMARY KEY (`schema_build`)
-) ENGINE=MyISAM;
+ `internal_schema_build` varchar(20) NOT NULL,
+ `external_schema_build` varchar(20) NOT NULL,
+ UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
+) 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) COLLATE latin1_bin NOT NULL DEFAULT '',
- `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `left_primer` varchar(100) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `right_primer` varchar(100) CHARACTER SET latin1 COLLATE latin1_bin 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') CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -383,28 +393,28 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `name` varchar(30) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -414,22 +424,22 @@ 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 ;
+) ENGINE=MyISAM AUTO_INCREMENT=82 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `table_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -439,71 +449,36 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
`max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
- `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `xref_id` int(10) unsigned NOT NULL,
+ `linkage_annotation` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin 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;
-
-CREATE TABLE `oligo_array` (
- `oligo_array_id` int(11) NOT NULL AUTO_INCREMENT,
- `parent_array_id` int(11) DEFAULT NULL,
- `probe_setsize` tinyint(4) NOT NULL DEFAULT '0',
- `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `type` enum('AFFY','OLIGO') COLLATE latin1_bin DEFAULT NULL,
- PRIMARY KEY (`oligo_array_id`)
-) ENGINE=MyISAM;
-
-CREATE TABLE `oligo_feature` (
- `oligo_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(11) NOT NULL DEFAULT '0',
- `seq_region_end` int(11) NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
- `mismatches` tinyint(4) DEFAULT NULL,
- `oligo_probe_id` int(11) NOT NULL DEFAULT '0',
- `analysis_id` int(11) NOT NULL DEFAULT '0',
- PRIMARY KEY (`oligo_feature_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
- KEY `probe_idx` (`oligo_probe_id`)
-) ENGINE=MyISAM;
-
-CREATE TABLE `oligo_probe` (
- `oligo_probe_id` int(11) NOT NULL AUTO_INCREMENT,
- `oligo_array_id` int(11) NOT NULL DEFAULT '0',
- `probeset` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `name` varchar(20) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin,
- `length` smallint(5) NOT NULL DEFAULT '0',
- PRIMARY KEY (`oligo_probe_id`,`oligo_array_id`),
- KEY `probeset_idx` (`probeset`),
- KEY `array_idx` (`oligo_array_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -512,7 +487,7 @@ CREATE TABLE `ontology_xref` (
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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon` (
`operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -530,7 +505,7 @@ 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 ;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -549,21 +524,21 @@ 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 ;
+) 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=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `peptide_seq` mediumtext CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -579,7 +554,7 @@ 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -588,11 +563,11 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -602,12 +577,12 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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 COLLATE latin1_bin,
+ `cigar_line` text CHARACTER SET latin1 COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
@@ -616,7 +591,7 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -625,27 +600,29 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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,
PRIMARY KEY (`protein_feature_id`),
KEY `translation_id` (`translation_id`),
KEY `hitname_index` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `qtl` (
`qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `trait` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `trait` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` float DEFAULT NULL,
`flank_marker_id_1` int(11) DEFAULT NULL,
`flank_marker_id_2` int(11) DEFAULT NULL,
`peak_marker_id` int(11) DEFAULT NULL,
PRIMARY KEY (`qtl_id`),
KEY `trait_idx` (`trait`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `qtl_feature` (
`seq_region_id` int(11) NOT NULL DEFAULT '0',
@@ -656,29 +633,29 @@ CREATE TABLE `qtl_feature` (
KEY `qtl_id` (`qtl_id`),
KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `qtl_synonym` (
`qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`qtl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source_database` enum('rat genome database','ratmap') COLLATE latin1_bin NOT NULL DEFAULT 'rat genome database',
- `source_primary_id` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `source_database` enum('rat genome database','ratmap') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'rat genome database',
+ `source_primary_id` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`qtl_synonym_id`),
KEY `qtl_idx` (`qtl_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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_consensus` text COLLATE latin1_bin,
+ `repeat_name` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_consensus` text CHARACTER SET latin1 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -695,32 +672,32 @@ 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 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 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) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1;
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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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_id` (`mapping_set_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -729,7 +706,7 @@ CREATE TABLE `seq_region_synonym` (
`external_db_id` smallint(5) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -737,35 +714,35 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin 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 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
- `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `new_stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin 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') CHARACTER SET latin1 COLLATE latin1_bin 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`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin 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`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -792,15 +769,15 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) 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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `transcript_idx` (`transcript_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -808,15 +785,15 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
`previous_exon_id` int(10) unsigned NOT NULL,
`next_exon_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin 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`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -832,15 +809,15 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) 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` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `value` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
KEY `type_val_idx` (`attrib_type_id`,`value`),
KEY `translation_idx` (`translation_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `unconventional_transcript_association` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -848,43 +825,43 @@ CREATE TABLE `unconventional_transcript_association` (
`interaction_type` enum('antisense','sense_intronic','sense_overlaping_exonic','chimeric_sense_exonic') DEFAULT NULL,
KEY `transcript_id` (`transcript_id`),
KEY `gene_id` (`gene_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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') CHARACTER SET latin1 COLLATE latin1_bin 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) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
`unmapped_reason_id` smallint(5) 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',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') CHARACTER SET latin1 COLLATE latin1_bin DEFAULT 'RawContig',
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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` smallint(5) 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
+ `full_description` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`external_db_id` int(11) NOT NULL DEFAULT '0',
- `dbprimary_acc` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `display_label` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `version` varchar(10) COLLATE latin1_bin NOT NULL DEFAULT '',
- `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 '',
+ `dbprimary_acc` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `display_label` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `version` varchar(10) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text CHARACTER SET latin1 COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+ `info_text` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin 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;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;