Initial import from ols-ensembl-loader

last pull: 2019-07-18 13:15 UTC
HEAD at commit: ad833efe2eed3646c891958b011f67af66cde627
last commit pertaining to sql/: 0636a37f2f3cae791cad91f9f7e91893325b4625

sql/tables.sql

+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2019] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+
+-- ---------------------------------------------------------------------
+-- The schema for the ensembl_ontology_NN database.
+-- ---------------------------------------------------------------------
+
+CREATE TABLE `meta` (
+  `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `meta_key` varchar(64) NOT NULL,
+  `meta_value` varchar(128) DEFAULT NULL,
+  `species_id` int(10) unsigned DEFAULT NULL,
+  PRIMARY KEY (`meta_id`),
+  UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+# Add schema type and schema version to the meta table
+INSERT INTO meta (meta_key, meta_value) VALUES
+  ('schema_type', 'ontology'),
+  ('schema_version', '98');
+
+# Patches included in this schema file
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_97_98_a.sql|schema_version');
+
+CREATE TABLE `ontology` (
+  `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `namespace` varchar(64) NOT NULL,
+  `data_version` varchar(64) DEFAULT NULL,
+  `title` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`ontology_id`),
+  UNIQUE KEY `ontology_name_namespace_idx` (`name`,`namespace`)
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+
+CREATE TABLE `subset` (
+  `subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `definition` varchar(511) NOT NULL DEFAULT '',
+  PRIMARY KEY (`subset_id`),
+  UNIQUE KEY `name` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+CREATE TABLE `term` (
+  `term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `ontology_id` int(10) unsigned NOT NULL,
+  `subsets` text,
+  `accession` varchar(64) NOT NULL,
+  `name` varchar(255) COLLATE utf8_general_ci NOT NULL,
+  `definition` text COLLATE utf8_general_ci,
+  `is_root` int(11) NOT NULL DEFAULT 0,
+  `is_obsolete` int(11) NOT NULL DEFAULT 0,
+  `iri` text,
+  PRIMARY KEY (`term_id`),
+  UNIQUE KEY `accession` (`accession`),
+  UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
+  KEY `term_name_idx` (`name`(100))
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+CREATE TABLE `synonym` (
+  `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `term_id` int(10) unsigned NOT NULL,
+  `name` text COLLATE utf8_general_ci NOT NULL,
+  `type` enum('EXACT','BROAD','NARROW','RELATED') DEFAULT NULL,
+  `dbxref` varchar(500) DEFAULT NULL,
+  PRIMARY KEY (`synonym_id`),
+  UNIQUE KEY `synonym_term_idx` (`term_id`,`synonym_id`),
+  KEY `synonym_name_idx` (`name`(100))
+) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+
+CREATE TABLE `alt_id` (
+  `alt_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `term_id` int(10) unsigned NOT NULL,
+  `accession` varchar(64) NOT NULL,
+  PRIMARY KEY (`alt_id`),
+  UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
+  KEY `ix_alt_id_accession` (`accession`)
+) ENGINE=MyISAM;
+
+CREATE TABLE `relation_type` (
+  `relation_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  PRIMARY KEY (`relation_type_id`),
+  UNIQUE KEY `name` (`name`)
+) ENGINE=MyISAM;
+
+
+CREATE TABLE `relation` (
+  `relation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `child_term_id` int(10) unsigned NOT NULL,
+  `parent_term_id` int(10) unsigned NOT NULL,
+  `relation_type_id` int(10) unsigned NOT NULL,
+  `intersection_of` tinyint(1) NOT NULL,
+  `ontology_id` int(10) unsigned NOT NULL,
+  PRIMARY KEY (`relation_id`),
+  UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`relation_type_id`,`intersection_of`,`ontology_id`),
+  KEY `ix_relation_parent_term_id` (`parent_term_id`),
+  KEY `ix_relation_relation_type_id` (`relation_type_id`),
+  KEY `ix_relation_ontology_id` (`ontology_id`)
+) ENGINE=MyISAM;
+
+
+CREATE TABLE `closure` (
+  `closure_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `child_term_id` int(10) unsigned NOT NULL,
+  `parent_term_id` int(10) unsigned NOT NULL,
+  `subparent_term_id` int(10) unsigned DEFAULT NULL,
+  `distance` tinyint(3) unsigned NOT NULL,
+  `ontology_id` int(10) unsigned NOT NULL,
+  `confident_relationship` tinyint(1) NOT NULL,
+  PRIMARY KEY (`closure_id`),
+  UNIQUE KEY `closure_child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
+  KEY `ix_closure_subparent_term_id` (`subparent_term_id`),
+  KEY `ix_closure_ontology_id` (`ontology_id`),
+  KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
+) ENGINE=MyISAM;
+
+-- There are additional tables in the released databases called
+-- "aux_XX_YY_map".  These are created by the "add_subset_maps.pl"
+-- scripts.  Please see the README document for further information.
+
+-- $Id$