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Commit 333e7159 authored by Marek Szuba's avatar Marek Szuba
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Test DB: sync the ontology database with the one from _ensembl_ 

For some reason ensembl-io test ontology database went out of sync some
time prior to release 97. See the discussion of PR #85.
parent 10427c1a
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2 merge requests!86Release-98 version bump,!86Release-98 version bump
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modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+ 169
− 167
View file @ 333e7159
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Mar 28 11:01:00 2017
-- Created on Mon Jun 17 16:51:58 2019
--
BEGIN TRANSACTION;
--
-- Table: alt_id
-- Table: "alt_id"
--
CREATE TABLE alt_id (
alt_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
term_id integer NOT NULL,
accession varchar(64) NOT NULL
CREATE TABLE "alt_id" (
"alt_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"term_id" integer NOT NULL,
"accession" varchar(64) NOT NULL
);
CREATE UNIQUE INDEX term_alt_idx ON alt_id (term_id, alt_id);
CREATE UNIQUE INDEX "term_alt_idx" ON "alt_id" ("term_id", "alt_id");
--
-- Table: aux_GO_Cross_product_review_map
-- Table: "aux_GO_Cross_product_review_map"
--
CREATE TABLE aux_GO_Cross_product_review_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_Cross_product_review_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx ON aux_GO_Cross_product_review_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx" ON "aux_GO_Cross_product_review_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_aspergillus_map
-- Table: "aux_GO_goslim_aspergillus_map"
--
CREATE TABLE aux_GO_goslim_aspergillus_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_aspergillus_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx02 ON aux_GO_goslim_aspergillus_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx02" ON "aux_GO_goslim_aspergillus_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_candida_map
-- Table: "aux_GO_goslim_candida_map"
--
CREATE TABLE aux_GO_goslim_candida_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_candida_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx03 ON aux_GO_goslim_candida_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx03" ON "aux_GO_goslim_candida_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_generic_map
-- Table: "aux_GO_goslim_generic_map"
--
CREATE TABLE aux_GO_goslim_generic_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_generic_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx04 ON aux_GO_goslim_generic_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx04" ON "aux_GO_goslim_generic_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_metagenomics_map
-- Table: "aux_GO_goslim_metagenomics_map"
--
CREATE TABLE aux_GO_goslim_metagenomics_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_metagenomics_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx05 ON aux_GO_goslim_metagenomics_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx05" ON "aux_GO_goslim_metagenomics_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_pir_map
-- Table: "aux_GO_goslim_pir_map"
--
CREATE TABLE aux_GO_goslim_pir_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_pir_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx06 ON aux_GO_goslim_pir_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx06" ON "aux_GO_goslim_pir_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_plant_map
-- Table: "aux_GO_goslim_plant_map"
--
CREATE TABLE aux_GO_goslim_plant_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_plant_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx07 ON aux_GO_goslim_plant_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx07" ON "aux_GO_goslim_plant_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_pombe_map
-- Table: "aux_GO_goslim_pombe_map"
--
CREATE TABLE aux_GO_goslim_pombe_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_pombe_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx08 ON aux_GO_goslim_pombe_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx08" ON "aux_GO_goslim_pombe_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_goslim_yeast_map
-- Table: "aux_GO_goslim_yeast_map"
--
CREATE TABLE aux_GO_goslim_yeast_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_goslim_yeast_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx09 ON aux_GO_goslim_yeast_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx09" ON "aux_GO_goslim_yeast_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_gosubset_prok_map
-- Table: "aux_GO_gosubset_prok_map"
--
CREATE TABLE aux_GO_gosubset_prok_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_gosubset_prok_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx10 ON aux_GO_gosubset_prok_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx10" ON "aux_GO_gosubset_prok_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_high_level_annotation_qc_map
-- Table: "aux_GO_high_level_annotation_qc_map"
--
CREATE TABLE aux_GO_high_level_annotation_qc_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_high_level_annotation_qc_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx11 ON aux_GO_high_level_annotation_qc_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx11" ON "aux_GO_high_level_annotation_qc_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_mf_needs_review_map
-- Table: "aux_GO_mf_needs_review_map"
--
CREATE TABLE aux_GO_mf_needs_review_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_mf_needs_review_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx12 ON aux_GO_mf_needs_review_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx12" ON "aux_GO_mf_needs_review_map" ("term_id", "subset_term_id");
--
-- Table: aux_GO_virus_checked_map
-- Table: "aux_GO_virus_checked_map"
--
CREATE TABLE aux_GO_virus_checked_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_GO_virus_checked_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx13 ON aux_GO_virus_checked_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx13" ON "aux_GO_virus_checked_map" ("term_id", "subset_term_id");
--
-- Table: aux_SO_DBVAR_map
-- Table: "aux_SO_DBVAR_map"
--
CREATE TABLE aux_SO_DBVAR_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_SO_DBVAR_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx14 ON aux_SO_DBVAR_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx14" ON "aux_SO_DBVAR_map" ("term_id", "subset_term_id");
--
-- Table: aux_SO_SOFA_map
-- Table: "aux_SO_SOFA_map"
--
CREATE TABLE aux_SO_SOFA_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_SO_SOFA_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx15 ON aux_SO_SOFA_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx15" ON "aux_SO_SOFA_map" ("term_id", "subset_term_id");
--
-- Table: aux_SO_biosapiens_map
-- Table: "aux_SO_biosapiens_map"
--
CREATE TABLE aux_SO_biosapiens_map (
term_id integer NOT NULL,
subset_term_id integer NOT NULL,
distance tinyint NOT NULL
CREATE TABLE "aux_SO_biosapiens_map" (
"term_id" integer NOT NULL,
"subset_term_id" integer NOT NULL,
"distance" tinyint NOT NULL
);
CREATE UNIQUE INDEX map_idx16 ON aux_SO_biosapiens_map (term_id, subset_term_id);
CREATE UNIQUE INDEX "map_idx16" ON "aux_SO_biosapiens_map" ("term_id", "subset_term_id");
--
-- Table: closure
-- Table: "closure"
--
CREATE TABLE closure (
closure_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
child_term_id integer NOT NULL,
parent_term_id integer NOT NULL,
subparent_term_id integer,
distance tinyint NOT NULL,
ontology_id integer NOT NULL,
confident_relationship tinyint NOT NULL DEFAULT 0
CREATE TABLE "closure" (
"closure_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"child_term_id" integer NOT NULL,
"parent_term_id" integer NOT NULL,
"subparent_term_id" integer,
"distance" tinyint NOT NULL,
"ontology_id" integer NOT NULL,
"confident_relationship" tinyint NOT NULL
);
CREATE UNIQUE INDEX child_parent_idx ON closure (child_term_id, parent_term_id, subparent_term_id, ontology_id);
CREATE UNIQUE INDEX "closure_child_parent_idx" ON "closure" ("child_term_id", "parent_term_id", "subparent_term_id", "ontology_id");
--
-- Table: meta
-- Table: "meta"
--
CREATE TABLE meta (
meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
meta_key varchar(64) NOT NULL,
meta_value varchar(128),
species_id integer
CREATE TABLE "meta" (
"meta_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"meta_key" varchar(64) NOT NULL,
"meta_value" varchar(128),
"species_id" integer
);
CREATE UNIQUE INDEX key_value_idx ON meta (meta_key, meta_value);
CREATE UNIQUE INDEX "key_value_idx" ON "meta" ("meta_key", "meta_value");
--
-- Table: ontology
-- Table: "ontology"
--
CREATE TABLE ontology (
ontology_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(64) NOT NULL,
namespace varchar(64) NOT NULL,
data_version varchar(64)
CREATE TABLE "ontology" (
"ontology_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"name" varchar(64) NOT NULL,
"namespace" varchar(64) NOT NULL,
"data_version" varchar(64),
"title" varchar(255)
);
CREATE UNIQUE INDEX name_namespace_idx ON ontology (name, namespace);
CREATE UNIQUE INDEX "ontology_name_namespace_idx" ON "ontology" ("name", "namespace");
--
-- Table: relation
-- Table: "relation"
--
CREATE TABLE relation (
relation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
child_term_id integer NOT NULL,
parent_term_id integer NOT NULL,
relation_type_id integer NOT NULL,
intersection_of tinyint NOT NULL DEFAULT 0,
ontology_id integer NOT NULL
CREATE TABLE "relation" (
"relation_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"child_term_id" integer NOT NULL,
"parent_term_id" integer NOT NULL,
"relation_type_id" integer NOT NULL,
"intersection_of" tinyint NOT NULL,
"ontology_id" integer NOT NULL
);
CREATE UNIQUE INDEX child_parent_idx02 ON relation (child_term_id, parent_term_id, relation_type_id, intersection_of, ontology_id);
CREATE UNIQUE INDEX "child_parent_idx" ON "relation" ("child_term_id", "parent_term_id", "relation_type_id", "intersection_of", "ontology_id");
--
-- Table: relation_type
-- Table: "relation_type"
--
CREATE TABLE relation_type (
relation_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(64) NOT NULL
CREATE TABLE "relation_type" (
"relation_type_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"name" varchar(64) NOT NULL
);
CREATE UNIQUE INDEX name_idx ON relation_type (name);
CREATE UNIQUE INDEX "name" ON "relation_type" ("name");
--
-- Table: subset
-- Table: "subset"
--
CREATE TABLE subset (
subset_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
name varchar(64) NOT NULL,
definition varchar(128) NOT NULL
CREATE TABLE "subset" (
"subset_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"name" varchar(64) NOT NULL,
"definition" varchar(1023) NOT NULL DEFAULT ''
);
CREATE UNIQUE INDEX name_idx02 ON subset (name);
CREATE UNIQUE INDEX "name02" ON "subset" ("name");
--
-- Table: synonym
-- Table: "synonym"
--
CREATE TABLE synonym (
synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
term_id integer NOT NULL,
name mediumtext NOT NULL,
type enum,
dbxref varchar(256) NOT NULL
CREATE TABLE "synonym" (
"synonym_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"term_id" integer NOT NULL,
"name" text NOT NULL,
"type" enum,
"dbxref" varchar(500)
);
CREATE UNIQUE INDEX term_synonym_idx ON synonym (term_id, synonym_id);
CREATE UNIQUE INDEX "synonym_term_idx" ON "synonym" ("term_id", "synonym_id");
--
-- Table: term
-- Table: "term"
--
CREATE TABLE term (
term_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
ontology_id integer NOT NULL,
subsets text,
accession varchar(64) NOT NULL,
name varchar(255) NOT NULL,
definition text,
is_root integer,
is_obsolete integer
CREATE TABLE "term" (
"term_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"ontology_id" integer NOT NULL,
"subsets" text,
"accession" varchar(64) NOT NULL,
"name" varchar(255) NOT NULL,
"definition" text,
"is_root" integer NOT NULL DEFAULT 0,
"is_obsolete" integer NOT NULL DEFAULT 0,
"iri" text
);
CREATE UNIQUE INDEX accession_idx ON term (accession);
CREATE UNIQUE INDEX "accession" ON "term" ("accession");
CREATE UNIQUE INDEX ontology_acc_idx ON term (ontology_id, accession);
CREATE UNIQUE INDEX "term_ontology_acc_idx" ON "term" ("ontology_id", "accession");
COMMIT;
modules/t/test-genome-DBs/ontology/ontology/ontology.txt
+ 6
− 6
View file @ 333e7159
1 GO biological_process releases/2016-03-30
2 GO cellular_component releases/2016-03-30
3 GO molecular_function releases/2016-03-30
5 SO sequence so-xp/releases/2015-11-24/so-xp.owl
6 EFO BrendaTissueOBO \N
7 EFO EFO \N
1 GO biological_process releases/2016-03-30 \N
2 GO cellular_component releases/2016-03-30 \N
3 GO molecular_function releases/2016-03-30 \N
5 SO sequence so-xp/releases/2015-11-24/so-xp.owl \N
6 EFO BrendaTissueOBO \N \N
7 EFO EFO \N \N
modules/t/test-genome-DBs/ontology/ontology/table.sql
+ 49
− 50
View file @ 333e7159
......@@ -4,7 +4,7 @@ CREATE TABLE `alt_id` (
`accession` varchar(64) NOT NULL,
PRIMARY KEY (`alt_id`),
UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
KEY `accession_idx` (`accession`(50))
KEY `ix_alt_id_accession` (`accession`)
) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_Cross_product_review_map` (
......@@ -12,112 +12,112 @@ CREATE TABLE `aux_GO_Cross_product_review_map` (
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_aspergillus_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_candida_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_generic_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_metagenomics_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_pir_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_plant_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_pombe_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_yeast_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_gosubset_prok_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_high_level_annotation_qc_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_mf_needs_review_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_virus_checked_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_DBVAR_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_SOFA_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_biosapiens_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `closure` (
`closure_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -126,31 +126,31 @@ CREATE TABLE `closure` (
`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 DEFAULT 0,
`confident_relationship` tinyint(1) NOT NULL,
PRIMARY KEY (`closure_id`),
UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_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 `ix_closure_ontology_id` (`ontology_id`),
KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
) ENGINE=MyISAM AUTO_INCREMENT=1453438 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`meta_key` varchar(64) CHARACTER SET latin1 NOT NULL,
`meta_value` varchar(128) CHARACTER SET latin1 DEFAULT NULL,
`species_id` int(1) unsigned DEFAULT NULL,
`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 AUTO_INCREMENT=47 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) CHARACTER SET latin1 NOT NULL,
`namespace` varchar(64) CHARACTER SET latin1 NOT NULL,
`data_version` varchar(64) CHARACTER SET latin1 DEFAULT NULL,
`title` varchar(255) CHARACTER SET latin1 DEFAULT NULL,
`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 `name_namespace_idx` (`name`,`namespace`)
UNIQUE KEY `ontology_name_namespace_idx` (`name`,`namespace`)
) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `relation` (
......@@ -158,11 +158,10 @@ CREATE TABLE `relation` (
`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(3) unsigned NOT NULL DEFAULT 0,
`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 `parent_idx` (`parent_term_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`)
......@@ -172,41 +171,41 @@ 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_idx` (`name`)
UNIQUE KEY `name` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
CREATE TABLE `subset` (
`subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) CHARACTER SET latin1 NOT NULL,
`name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
`definition` varchar(1023) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
PRIMARY KEY (`subset_id`),
UNIQUE KEY `name_idx` (`name`)
UNIQUE KEY `name` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=18 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` mediumtext CHARACTER SET utf8 COLLATE utf8_swedish_ci NOT NULL,
`type` enum('EXACT','BROAD','NARROW','RELATED') CHARACTER SET utf8 COLLATE utf8_swedish_ci DEFAULT NULL,
`dbxref` varchar(256) CHARACTER SET utf8 COLLATE utf8_swedish_ci 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 `term_synonym_idx` (`term_id`,`synonym_id`),
KEY `name_idx` (`name`(50))
UNIQUE KEY `synonym_term_idx` (`term_id`,`synonym_id`),
KEY `synonym_name_idx` (`name`(100))
) ENGINE=MyISAM AUTO_INCREMENT=104283 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 CHARACTER SET latin1 DEFAULT NULL,
`accession` varchar(64) CHARACTER SET latin1 NOT NULL,
`name` varchar(255) CHARACTER SET latin1 NOT NULL,
`definition` text CHARACTER SET latin1 DEFAULT NULL,
`is_root` int(11) DEFAULT NULL,
`is_obsolete` int(11) DEFAULT NULL,
`iri` text CHARACTER SET latin1 DEFAULT NULL,
`subsets` text COLLATE utf8_unicode_ci DEFAULT NULL,
`accession` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
`name` varchar(255) CHARACTER SET utf8 NOT NULL,
`definition` text CHARACTER SET utf8 DEFAULT NULL,
`is_root` int(11) NOT NULL DEFAULT 0,
`is_obsolete` int(11) NOT NULL DEFAULT 0,
`iri` text COLLATE utf8_unicode_ci DEFAULT NULL,
PRIMARY KEY (`term_id`),
UNIQUE KEY `accession_idx` (`accession`),
UNIQUE KEY `ontology_acc_idx` (`ontology_id`,`accession`),
KEY `name_idx` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=44356 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
UNIQUE KEY `accession` (`accession`),
UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
KEY `term_name_idx` (`name`(100))
) ENGINE=MyISAM AUTO_INCREMENT=45001 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
modules/t/test-genome-DBs/ontology/ontology/term.txt
+ 168
− 165
View file @ 333e7159
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