This SQL file will create an empty ensembl_ontology_NN database.

Currently drops each table before (re-)creating it.

misc-scripts/ontology/sql/table.sql

+DROP TABLE IF EXISTS ontology;
+CREATE TABLE ontology (
+  ontology_id   INT UNSIGNED NOT NULL AUTO_INCREMENT,
+  name          VARCHAR(64) NOT NULL,
+  namespace     VARCHAR(64) NOT NULL,
+
+  PRIMARY KEY (ontology_id),
+  UNIQUE INDEX name_namespace_idx (name, namespace)
+);
+
+DROP TABLE IF EXISTS term;
+CREATE TABLE term (
+  term_id       INT UNSIGNED NOT NULL AUTO_INCREMENT,
+  ontology_id   INT UNSIGNED NOT NULL,
+  accession     CHAR(10) NOT NULL,
+  name          VARCHAR(255) NOT NULL,
+  definition    TEXT,
+
+  PRIMARY KEY (term_id),
+  INDEX ontology_idx (ontology_id),
+  UNIQUE INDEX acc_ontology_idx (accession, ontology_id)
+);
+
+DROP TABLE IF EXISTS relation_type;
+CREATE TABLE relation_type (
+  relation_type_id  INT UNSIGNED NOT NULL AUTO_INCREMENT,
+  name              VARCHAR(24) NOT NULL,
+
+  PRIMARY KEY (relation_type_id),
+  UNIQUE INDEX name_idx (name)
+);
+
+DROP TABLE IF EXISTS relation;
+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,
+
+  PRIMARY KEY (relation_id),
+  UNIQUE INDEX child_parent_idx (child_term_id, parent_term_id),
+  INDEX parent_idx (parent_term_id)
+);
+
+DROP TABLE IF EXISTS closure;
+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,
+  distance          TINYINT UNSIGNED NOT NULL,
+  subparent_term_id INT UNSIGNED,
+
+  PRIMARY KEY (closure_id),
+  UNIQUE INDEX parent_child_idx
+    (parent_term_id, child_term_id, subparent_term_id),
+  INDEX child_distance_idx (child_term_id, distance)
+);