From 610a69fca1a0e99a7d36cc55c3ee2167381e2bf7 Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Wed, 19 Dec 2018 09:39:31 +0000
Subject: [PATCH] Updated SQL tables script with all updates
---
misc-scripts/ontology/sql/patch_95_96_b.sql | 4 +-
misc-scripts/ontology/sql/tables.sql | 203 ++++++++++----------
2 files changed, 102 insertions(+), 105 deletions(-)
diff --git a/misc-scripts/ontology/sql/patch_95_96_b.sql b/misc-scripts/ontology/sql/patch_95_96_b.sql
index 50886e7f0e..92934a805d 100644
--- a/misc-scripts/ontology/sql/patch_95_96_b.sql
+++ b/misc-scripts/ontology/sql/patch_95_96_b.sql
@@ -21,6 +21,6 @@
-- Added fields to Term and Ontology tables
-- Added columns
-ALTER TABLE ontology ADD COLUMN `title` varchar(255) NULL;
+ALTER TABLE ontology ADD COLUMN `title` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL;
-ALTER TABLE term ADD COLUMN `iri` varchar(1000) NULL;
+ALTER TABLE term ADD COLUMN `iri` text NULL;
diff --git a/misc-scripts/ontology/sql/tables.sql b/misc-scripts/ontology/sql/tables.sql
index b4c7873b0d..00a7d783d7 100644
--- a/misc-scripts/ontology/sql/tables.sql
+++ b/misc-scripts/ontology/sql/tables.sql
@@ -18,15 +18,14 @@
-- The schema for the ensembl_ontology_NN database.
-- ---------------------------------------------------------------------
-CREATE TABLE meta (
- meta_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- meta_key VARCHAR(64) NOT NULL,
- meta_value VARCHAR(128),
- species_id INT UNSIGNED DEFAULT NULL,
-
- PRIMARY KEY (meta_id),
- UNIQUE INDEX key_value_idx (meta_key, meta_value)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+CREATE TABLE `meta` (
+ `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `meta_key` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `meta_value` varchar(128) COLLATE utf8_unicode_ci 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
@@ -38,100 +37,98 @@ INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_95_96_a.sql|schema_version');
-CREATE TABLE ontology (
- ontology_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- name VARCHAR(64) NOT NULL,
- namespace VARCHAR(64) NOT NULL,
- data_version VARCHAR(64) DEFAULT NULL,
- `title` varchar(255) NULL,
- PRIMARY KEY (ontology_id),
- UNIQUE INDEX name_namespace_idx (name, namespace)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE subset (
- subset_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- name VARCHAR(64) NOT NULL,
- definition VARCHAR(128) NOT NULL,
-
- PRIMARY KEY (subset_id),
- UNIQUE INDEX name_idx (name)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE term (
- term_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- ontology_id INT UNSIGNED NOT NULL,
- subsets TEXT,
- accession VARCHAR(64) NOT NULL,
- name VARCHAR(255) NOT NULL,
- definition TEXT,
- is_root INT NOT NULL DEFAULT 0,
- is_obsolete INT NOT NULL DEFAULT 0,
- `iri` varchar(1000) NULL,
- PRIMARY KEY (term_id),
- UNIQUE INDEX accession_idx (accession),
- UNIQUE INDEX ontology_acc_idx (ontology_id, accession),
- INDEX name_idx (name)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE synonym (
- synonym_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- term_id INT UNSIGNED NOT NULL,
- name TEXT NOT NULL,
- type ENUM('EXACT', 'BROAD', 'NARROW', 'RELATED'),
- dbxref VARCHAR(258) NULL,
-
- PRIMARY KEY (synonym_id),
- UNIQUE INDEX term_synonym_idx (term_id, synonym_id),
- INDEX name_idx (name(50))
-) COLLATE=utf8_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE alt_id (
- alt_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- term_id INT UNSIGNED NOT NULL,
- accession VARCHAR(64) NOT NULL,
-
- PRIMARY KEY (alt_id),
- UNIQUE INDEX term_alt_idx (term_id, alt_id),
- INDEX accession_idx (accession(50))
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE relation_type (
- relation_type_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- name VARCHAR(64) NOT NULL,
-
- PRIMARY KEY (relation_type_id),
- UNIQUE INDEX name_idx (name)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE relation (
- relation_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- child_term_id INT UNSIGNED NOT NULL,
- parent_term_id INT UNSIGNED NOT NULL,
- relation_type_id INT UNSIGNED NOT NULL,
- intersection_of TINYINT UNSIGNED NOT NULL DEFAULT 0,
- ontology_id INT UNSIGNED NOT NULL,
-
- PRIMARY KEY (relation_id),
- UNIQUE INDEX child_parent_idx
- (child_term_id, parent_term_id, relation_type_id, intersection_of, ontology_id),
- INDEX parent_idx (parent_term_id)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-CREATE TABLE closure (
- closure_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- child_term_id INT UNSIGNED NOT NULL,
- parent_term_id INT UNSIGNED NOT NULL,
- subparent_term_id INT UNSIGNED,
- distance TINYINT UNSIGNED NOT NULL,
- ontology_id INT UNSIGNED NOT NULL,
- confident_relationship BOOL NOT NULL DEFAULT 0,
-
- PRIMARY KEY (closure_id),
- UNIQUE INDEX child_parent_idx
- (child_term_id, parent_term_id, subparent_term_id, ontology_id),
- INDEX parent_subparent_idx
- (parent_term_id, subparent_term_id)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+CREATE TABLE `ontology` (
+ `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `namespace` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `data_version` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
+ `title` varchar(255) COLLATE utf8_unicode_ci 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) COLLATE utf8_unicode_ci NOT NULL,
+ `definition` varchar(511) COLLATE utf8_unicode_ci 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) NOT NULL,
+ `definition` text,
+ `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;
+
+CREATE TABLE `synonym` (
+ `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `term_id` int(10) unsigned NOT NULL,
+ `name` text CHARACTER SET utf8 NOT NULL,
+ `type` enum('EXACT','BROAD','NARROW','RELATED') COLLATE utf8_unicode_ci DEFAULT NULL,
+ `dbxref` varchar(500) COLLATE utf8_unicode_ci 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 DEFAULT CHARSET=utf8;
+
+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 DEFAULT CHARSET=utf8;
+
+
+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 DEFAULT CHARSET=utf8;
+
+
+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 DEFAULT CHARSET=utf8;
-- There are additional tables in the released databases called
-- "aux_XX_YY_map". These are created by the "add_subset_maps.pl"
--
GitLab