Commit 589c8c6c authored by Andy Yates's avatar Andy Yates
Browse files

updating to the newest release of ensembl 73

parent c16a39f0
3 \N patch patch_71_72_a.sql|schema_version
4 \N patch patch_71_72_b.sql|associated_xref
58 \N patch patch_72_73_a.sql|schema_version
59 \N patch patch_72_73_b.sql|alt_allele_type
60 \N patch patch_72_73_c.sql|add_object_type_marker
1 \N schema_type core
2 \N schema_version 72
2 \N schema_version 73
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
......
......@@ -34,4 +34,6 @@
79 \N patch patch_70_71_b.sql|mapping_set_index
80 \N patch patch_71_72_a.sql|schema_version
81 \N patch patch_71_72_b.sql|associated_xref
82 \N patch patch_72_73_a.sql|schema_version
82 \N patch patch_72_73_a.sql|schema_version
83 \N patch patch_72_73_b.sql|alt_allele_type
84 \N patch patch_72_73_c.sql|add_object_type_marker
......@@ -515,7 +515,7 @@ CREATE TABLE `misc_set` (
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',
`ensembl_object_type` enum('RawContig', 'Transcript', 'Gene', 'Translation', 'Operon', 'OperonTranscript', 'Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
......
1 \N schema_version 72
1 \N schema_version 73
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
......@@ -34,3 +34,6 @@
83 \N patch patch_70_71_b.sql|mapping_set_index
84 \N patch patch_71_72_a.sql|schema_version
85 \N patch patch_71_72_b.sql|associated_xref
86 \N patch patch_72_73_a.sql|schema_version
87 \N patch patch_72_73_b.sql|alt_allele_type
88 \N patch patch_72_73_c.sql|add_object_type_marker
CREATE TABLE `alt_allele` (
`alt_allele_id` int(11) NOT NULL AUTO_INCREMENT,
`gene_id` int(11) NOT NULL DEFAULT '0',
`is_ref` tinyint(1) NOT NULL DEFAULT '0',
UNIQUE KEY `gene_idx` (`gene_id`),
UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
`alt_allele_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`alt_allele_group_id` int(10) unsigned NOT NULL,
`gene_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`alt_allele_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
`attrib` enum('IS_REPRESENTATIVE','IS_MOST_COMMON_ALLELE','IN_CORRECTED_ASSEMBLY','HAS_CODING_POTENTIAL','IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY','IN_SYNTENIC_REGION','HAS_SAME_UNDERLYING_DNA_SEQUENCE','IN_BROKEN_ASSEMBLY_REGION','IS_VALID_ALTERNATE','SAME_AS_REPRESENTATIVE','SAME_AS_ANOTHER_ALLELE','MANUALLY_ASSIGNED','AUTOMATICALLY_ASSIGNED') DEFAULT NULL,
KEY `aa_idx` (`alt_allele_id`,`attrib`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
......@@ -447,7 +458,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=86 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=89 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -494,7 +505,7 @@ CREATE TABLE `misc_set` (
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') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
`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,
......
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