ontology updated for release 85

misc-scripts/ontology/sql/patch_84_85_a.sql

+-- Copyright [1999-2016] Wellcome Trust Sanger Institute and the 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.
+
+# patch_84_85_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 85.
+
+UPDATE meta SET meta_value='85' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_84_85_a.sql|schema_version');

misc-scripts/ontology/sql/tables.sql

@@ -30,11 +30,15 @@ CREATE TABLE meta (
 # Add schema type and schema version to the meta table
 INSERT INTO meta (meta_key, meta_value) VALUES 
   ('schema_type', 'ontology'),
-  ('schema_version', '84');
+  ('schema_version', '85');
 
 # Patches included in this schema file
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_83_84_a.sql|schema_version');
+  VALUES ('patch', 'patch_84_85_a.sql|schema_version');
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_84_85_b.sql|confident_relationship');
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_84_85_c.sql| add synonym dbxref');
 
 
 CREATE TABLE ontology (
@@ -76,6 +80,7 @@ CREATE TABLE synonym (
   term_id       INT UNSIGNED NOT NULL,
   name          TEXT NOT NULL,
   type		ENUM('EXACT', 'BROAD', 'NARROW', 'RELATED'),
+  dbxref        VARCHAR(64)  NULL,
 
   PRIMARY KEY (synonym_id),
   UNIQUE INDEX term_synonym_idx (term_id, synonym_id),
@@ -121,6 +126,7 @@ CREATE TABLE closure (
   subparent_term_id INT UNSIGNED,
   distance          TINYINT UNSIGNED NOT NULL,
   ontology_id       INT UNSIGNED NOT NULL,
+  confident_relationship BOOL NOT NULL,
 
   PRIMARY KEY (closure_id),
   UNIQUE INDEX child_parent_idx

modules/t/test-genome-DBs/ontology/ontology/meta.txt

@@ -9,7 +9,7 @@
 10	patch	patch_72_73_b.sql|meta	\N
 12	patch	patch_73_74_a.sql|schema_version	\N
 14	patch	patch_74_75_a.sql|schema_version	\N
-15	schema_version	84	\N
+15	schema_version	85	\N
 16	patch	patch_75_76_a.sql|schema_version	\N
 17	patch	patch_76_77_a.sql|schema_version	\N
 18	patch	patch_77_78_a.sql|schema_version	\N
@@ -22,3 +22,4 @@
 25	patch	patch_83_84_a.sql|schema_version	\N
 26	patch	patch_84_85_b.sql|confident_relationship	\N
 27	patch	patch_84_85_c.sql| add synonym dbxref	\N
+28	patch	patch_84_85_a.sql|schema_version	\N