mirror of
https://github.com/biopython/biopython.git
synced 2025-10-21 06:23:48 +08:00
9f7eed8a1f
Fix for GitHub issue #741 by changing the sqlite3 database schema to use foreign keys. A new test has been added in that explicitly tests to make sure associated data with a bioentry is removed. To accommodate the use of foreign keys the connection to an sqlite database must set the PRAGMA, which is now done automatically when opening the database. The upstream BioSQL schema for sqlite3 has also been updated, see https://github.com/biosql/biosql/pull/3
398 lines
14 KiB
SQL
398 lines
14 KiB
SQL
-- BioSQL database schema for SQLite.
|
|
--
|
|
-- This file is part of BioSQL.
|
|
--
|
|
-- BioSQL is free software: you can redistribute it and/or modify it
|
|
-- under the terms of the GNU Lesser General Public License as
|
|
-- published by the Free Software Foundation, either version 3 of the
|
|
-- License, or (at your option) any later version.
|
|
--
|
|
-- BioSQL is distributed in the hope that it will be useful,
|
|
-- but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
-- GNU Lesser General Public License for more details.
|
|
--
|
|
-- You should have received a copy of the GNU Lesser General Public License
|
|
-- along with BioSQL. If not, see <http://www.gnu.org/licenses/>.
|
|
--
|
|
-- ========================================================================
|
|
--
|
|
-- See MySQL database schema and BioSQL website for table documentation.
|
|
-- This contains notes specific to SQLite
|
|
--
|
|
-- A note about Primary Keys in SQLite
|
|
-- SQLite automatically creates a ROWID for each row of a table.
|
|
-- Using this ROWID as the primary key is faster than using a
|
|
-- user-defined primary key. By declaring a column as an
|
|
-- INTEGER PRIMARY KEY, you are actually creating an alias to the
|
|
-- ROWID and get the associated speed benefits. The ROWID effectively
|
|
-- "autoincrements"; however, it can reuse ROWIDs of deleted rows.
|
|
-- To avoid reusing old ROWIDs would require adding the AUTOINCREMENT
|
|
-- keyword, which also reduces the performance.
|
|
-- ( see http://www.sqlite.org/autoinc.html)
|
|
|
|
CREATE TABLE biodatabase (
|
|
biodatabase_id INTEGER PRIMARY KEY,
|
|
name VARCHAR(128) NOT NULL,
|
|
authority VARCHAR(128),
|
|
description TEXT,
|
|
UNIQUE (name)
|
|
);
|
|
|
|
CREATE INDEX db_auth on biodatabase(authority);
|
|
|
|
CREATE TABLE taxon (
|
|
taxon_id INTEGER PRIMARY KEY,
|
|
ncbi_taxon_id INT(10),
|
|
parent_taxon_id INT(10) ,
|
|
node_rank VARCHAR(32),
|
|
genetic_code TINYINT ,
|
|
mito_genetic_code TINYINT ,
|
|
left_value INT(10) ,
|
|
right_value INT(10) ,
|
|
UNIQUE (ncbi_taxon_id),
|
|
UNIQUE (left_value),
|
|
UNIQUE (right_value)
|
|
);
|
|
|
|
CREATE INDEX taxparent ON taxon(parent_taxon_id);
|
|
|
|
CREATE TABLE taxon_name (
|
|
taxon_id INTEGER,
|
|
name VARCHAR(255) NOT NULL,
|
|
name_class VARCHAR(32) NOT NULL,
|
|
UNIQUE (taxon_id,name,name_class),
|
|
FOREIGN KEY ( taxon_id ) REFERENCES taxon ( taxon_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX taxnametaxonid ON taxon_name(taxon_id);
|
|
CREATE INDEX taxnamename ON taxon_name(name);
|
|
|
|
CREATE TABLE ontology (
|
|
ontology_id INTEGER PRIMARY KEY,
|
|
name VARCHAR(32) NOT NULL,
|
|
definition TEXT,
|
|
UNIQUE (name)
|
|
);
|
|
|
|
CREATE TABLE term (
|
|
term_id INTEGER PRIMARY KEY,
|
|
name VARCHAR(255) NOT NULL,
|
|
definition TEXT,
|
|
identifier VARCHAR(40) ,
|
|
is_obsolete CHAR(1),
|
|
ontology_id INTEGER,
|
|
UNIQUE (identifier),
|
|
UNIQUE (name,ontology_id,is_obsolete),
|
|
FOREIGN KEY ( ontology_id ) REFERENCES ontology ( ontology_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX term_ont ON term(ontology_id);
|
|
|
|
CREATE TABLE term_synonym (
|
|
synonym VARCHAR(255) NOT NULL,
|
|
term_id INTEGER,
|
|
PRIMARY KEY (term_id,synonym),
|
|
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE TABLE term_dbxref (
|
|
term_id INTEGER,
|
|
dbxref_id INTEGER,
|
|
rank SMALLINT,
|
|
PRIMARY KEY (term_id, dbxref_id),
|
|
|
|
FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX trmdbxref_dbxrefid ON term_dbxref(dbxref_id);
|
|
|
|
CREATE TABLE term_relationship (
|
|
term_relationship_id INTEGER PRIMARY KEY,
|
|
subject_term_id INTEGER,
|
|
predicate_term_id INTEGER,
|
|
object_term_id INTEGER,
|
|
ontology_id INTEGER,
|
|
UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id),
|
|
|
|
FOREIGN KEY ( subject_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
|
|
FOREIGN KEY ( predicate_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
|
|
FOREIGN KEY ( object_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
|
|
FOREIGN KEY ( ontology_id ) REFERENCES ontology ( ontology_id ) ON DELETE CASCADE
|
|
|
|
);
|
|
|
|
CREATE INDEX trmrel_predicateid ON term_relationship(predicate_term_id);
|
|
CREATE INDEX trmrel_objectid ON term_relationship(object_term_id);
|
|
CREATE INDEX trmrel_ontid ON term_relationship(ontology_id);
|
|
|
|
CREATE TABLE term_relationship_term (
|
|
term_relationship_id INTEGER PRIMARY KEY,
|
|
term_id INTEGER,
|
|
UNIQUE ( term_id ),
|
|
|
|
FOREIGN KEY (term_relationship_id) REFERENCES term_relationship(term_relationship_id) ON DELETE CASCADE,
|
|
FOREIGN KEY (term_id) REFERENCES term(term_id) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE TABLE term_path (
|
|
term_path_id INTEGER PRIMARY KEY,
|
|
subject_term_id INTEGER,
|
|
predicate_term_id INTEGER,
|
|
object_term_id INTEGER,
|
|
ontology_id INTEGER,
|
|
distance INT(10) ,
|
|
UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id,distance),
|
|
FOREIGN KEY ( subject_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
|
|
FOREIGN KEY ( predicate_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
|
|
FOREIGN KEY ( object_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
|
|
FOREIGN KEY ( ontology_id ) REFERENCES ontology ( ontology_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX trmpath_predicateid ON term_path(predicate_term_id);
|
|
CREATE INDEX trmpath_objectid ON term_path(object_term_id);
|
|
CREATE INDEX trmpath_ontid ON term_path(ontology_id);
|
|
|
|
CREATE TABLE bioentry (
|
|
bioentry_id INTEGER PRIMARY KEY,
|
|
biodatabase_id INTEGER,
|
|
taxon_id INT(10) ,
|
|
name VARCHAR(40) NOT NULL,
|
|
accession VARCHAR(128) NOT NULL,
|
|
identifier VARCHAR(40) ,
|
|
division VARCHAR(6),
|
|
description TEXT,
|
|
version SMALLINT NOT NULL,
|
|
UNIQUE (accession,biodatabase_id,version),
|
|
UNIQUE (identifier, biodatabase_id),
|
|
|
|
FOREIGN KEY ( taxon_id ) REFERENCES taxon ( taxon_id ),
|
|
FOREIGN KEY ( biodatabase_id ) REFERENCES biodatabase ( biodatabase_id )
|
|
);
|
|
|
|
CREATE INDEX bioentry_name ON bioentry(name);
|
|
CREATE INDEX bioentry_db ON bioentry(biodatabase_id);
|
|
CREATE INDEX bioentry_tax ON bioentry(taxon_id);
|
|
|
|
CREATE TABLE bioentry_relationship (
|
|
bioentry_relationship_id INTEGER PRIMARY KEY,
|
|
object_bioentry_id INTEGER,
|
|
subject_bioentry_id INTEGER,
|
|
term_id INTEGER,
|
|
rank INT(5),
|
|
UNIQUE (object_bioentry_id,subject_bioentry_id,term_id),
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( object_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( subject_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX bioentryrel_trm ON bioentry_relationship(term_id);
|
|
CREATE INDEX bioentryrel_child ON bioentry_relationship(subject_bioentry_id);
|
|
|
|
CREATE TABLE bioentry_path (
|
|
object_bioentry_id INTEGER PRIMARY KEY,
|
|
subject_bioentry_id INTEGER,
|
|
term_id INTEGER,
|
|
distance INT(10) ,
|
|
UNIQUE (object_bioentry_id,subject_bioentry_id,term_id,distance),
|
|
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
|
|
FOREIGN KEY ( object_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( subject_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX bioentrypath_trm ON bioentry_path(term_id);
|
|
CREATE INDEX bioentrypath_child ON bioentry_path(subject_bioentry_id);
|
|
|
|
CREATE TABLE biosequence (
|
|
bioentry_id INTEGER PRIMARY KEY,
|
|
version SMALLINT,
|
|
length INT(10),
|
|
alphabet VARCHAR(10),
|
|
seq LONGTEXT,
|
|
FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE TABLE dbxref (
|
|
dbxref_id INTEGER PRIMARY KEY,
|
|
dbname VARCHAR(40) NOT NULL,
|
|
accession VARCHAR(128) NOT NULL,
|
|
version SMALLINT NOT NULL,
|
|
UNIQUE(accession, dbname, version)
|
|
);
|
|
|
|
CREATE INDEX dbxref_db ON dbxref(dbname);
|
|
|
|
CREATE TABLE dbxref_qualifier_value (
|
|
dbxref_id INTEGER,
|
|
term_id INTEGER,
|
|
rank SMALLINT NOT NULL DEFAULT 0,
|
|
value TEXT,
|
|
PRIMARY KEY (dbxref_id,term_id,rank),
|
|
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX dbxrefqual_dbx ON dbxref_qualifier_value(dbxref_id);
|
|
CREATE INDEX dbxrefqual_trm ON dbxref_qualifier_value(term_id);
|
|
|
|
CREATE TABLE bioentry_dbxref (
|
|
bioentry_id INTEGER,
|
|
dbxref_id INTEGER,
|
|
rank SMALLINT,
|
|
PRIMARY KEY (bioentry_id,dbxref_id),
|
|
FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE
|
|
|
|
);
|
|
|
|
CREATE INDEX dblink_dbx ON bioentry_dbxref(dbxref_id);
|
|
|
|
CREATE TABLE reference (
|
|
reference_id INTEGER PRIMARY KEY,
|
|
dbxref_id INT(10) ,
|
|
location TEXT NOT NULL,
|
|
title TEXT,
|
|
authors TEXT,
|
|
crc VARCHAR(32),
|
|
UNIQUE (dbxref_id),
|
|
UNIQUE (crc),
|
|
FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id )
|
|
);
|
|
|
|
CREATE TABLE bioentry_reference (
|
|
bioentry_id INTEGER,
|
|
reference_id INTEGER,
|
|
start_pos INT(10),
|
|
end_pos INT(10),
|
|
rank SMALLINT NOT NULL DEFAULT 0,
|
|
PRIMARY KEY(bioentry_id,reference_id,rank),
|
|
FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
|
|
FOREIGN KEY ( reference_id ) REFERENCES reference ( reference_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX bioentryref_ref ON bioentry_reference(reference_id);
|
|
|
|
CREATE TABLE comment (
|
|
comment_id INTEGER PRIMARY KEY,
|
|
bioentry_id INTEGER,
|
|
comment_text TEXT NOT NULL,
|
|
rank SMALLINT NOT NULL DEFAULT 0,
|
|
UNIQUE(bioentry_id, rank),
|
|
FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE TABLE bioentry_qualifier_value (
|
|
bioentry_id INTEGER,
|
|
term_id INTEGER,
|
|
value TEXT,
|
|
rank INT(5) NOT NULL DEFAULT 0,
|
|
UNIQUE (bioentry_id,term_id,rank),
|
|
FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
|
|
);
|
|
|
|
CREATE INDEX bioentryqual_trm ON bioentry_qualifier_value(term_id);
|
|
|
|
CREATE TABLE seqfeature (
|
|
seqfeature_id INTEGER PRIMARY KEY,
|
|
bioentry_id INTEGER,
|
|
type_term_id INTEGER,
|
|
source_term_id INTEGER,
|
|
display_name VARCHAR(64),
|
|
rank SMALLINT NOT NULL DEFAULT 0,
|
|
UNIQUE (bioentry_id,type_term_id,source_term_id,rank),
|
|
FOREIGN KEY ( type_term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( source_term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX seqfeature_trm ON seqfeature(type_term_id);
|
|
CREATE INDEX seqfeature_fsrc ON seqfeature(source_term_id);
|
|
|
|
CREATE TABLE seqfeature_relationship (
|
|
seqfeature_relationship_id INTEGER PRIMARY KEY,
|
|
object_seqfeature_id INTEGER,
|
|
subject_seqfeature_id INTEGER,
|
|
term_id INTEGER,
|
|
rank INT(5),
|
|
UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id),
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( object_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( subject_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX seqfeaturerel_trm ON seqfeature_relationship(term_id);
|
|
CREATE INDEX seqfeaturerel_child ON seqfeature_relationship(subject_seqfeature_id);
|
|
|
|
CREATE TABLE seqfeature_path (
|
|
object_seqfeature_id INTEGER,
|
|
subject_seqfeature_id INTEGER,
|
|
term_id INTEGER,
|
|
distance INT(10) ,
|
|
UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id,distance),
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( object_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( subject_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX seqfeaturepath_trm ON seqfeature_path(term_id);
|
|
CREATE INDEX seqfeaturepath_child ON seqfeature_path(subject_seqfeature_id);
|
|
|
|
CREATE TABLE seqfeature_qualifier_value (
|
|
seqfeature_id INTEGER,
|
|
term_id INTEGER,
|
|
rank SMALLINT NOT NULL DEFAULT 0,
|
|
value TEXT NOT NULL,
|
|
PRIMARY KEY (seqfeature_id,term_id,rank),
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
|
|
FOREIGN KEY ( seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX seqfeaturequal_trm ON seqfeature_qualifier_value(term_id);
|
|
|
|
CREATE TABLE seqfeature_dbxref (
|
|
seqfeature_id INTEGER,
|
|
dbxref_id INTEGER,
|
|
rank SMALLINT,
|
|
PRIMARY KEY (seqfeature_id,dbxref_id),
|
|
FOREIGN KEY ( seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE
|
|
);
|
|
|
|
CREATE INDEX feadblink_dbx ON seqfeature_dbxref(dbxref_id);
|
|
|
|
CREATE TABLE location (
|
|
location_id INTEGER PRIMARY KEY,
|
|
seqfeature_id INTEGER,
|
|
dbxref_id INT(10),
|
|
term_id INT(10),
|
|
start_pos INT(10),
|
|
end_pos INT(10),
|
|
strand TINYINT NOT NULL DEFAULT 0,
|
|
rank SMALLINT NOT NULL DEFAULT 0,
|
|
UNIQUE (seqfeature_id, rank),
|
|
FOREIGN KEY ( seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ),
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
|
|
);
|
|
|
|
CREATE INDEX seqfeatureloc_start ON location(start_pos, end_pos);
|
|
CREATE INDEX seqfeatureloc_dbx ON location(dbxref_id);
|
|
CREATE INDEX seqfeatureloc_trm ON location(term_id);
|
|
|
|
CREATE TABLE location_qualifier_value (
|
|
location_id INTEGER,
|
|
term_id INTEGER,
|
|
value VARCHAR(255) NOT NULL,
|
|
int_value INT(10),
|
|
PRIMARY KEY (location_id,term_id),
|
|
FOREIGN KEY ( location_id ) REFERENCES location ( location_id ) ON DELETE CASCADE,
|
|
FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
|
|
);
|
|
|
|
CREATE INDEX locationqual_trm ON location_qualifier_value(term_id);
|