/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.0/GO_DB.sql is in r-bioc-annotationdbi 1.26.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
CREATE TABLE go_ontology (
ontology VARCHAR(9) PRIMARY KEY, -- GO ontology (short label)
term_type VARCHAR(18) NOT NULL UNIQUE -- GO ontology (full label)
);
CREATE TABLE go_term (
_id INTEGER PRIMARY KEY,
go_id CHAR(10) NOT NULL UNIQUE, -- GO ID
term VARCHAR(255) NOT NULL, -- textual label for the GO term
ontology VARCHAR(9) NOT NULL, -- REFERENCES go_ontology
definition TEXT NULL, -- textual definition for the GO term
FOREIGN KEY (ontology) REFERENCES go_ontology (ontology)
);
CREATE TABLE sqlite_stat1(tbl,idx,stat);
CREATE TABLE go_obsolete (
go_id CHAR(10) PRIMARY KEY, -- GO ID
term VARCHAR(255) NOT NULL, -- textual label for the GO term
ontology VARCHAR(9) NOT NULL, -- REFERENCES go_ontology
definition TEXT NULL, -- textual definition for the GO term
FOREIGN KEY (ontology) REFERENCES go_ontology (ontology)
);
CREATE TABLE go_synonym (
_id INTEGER NOT NULL, -- REFERENCES go_term
synonym VARCHAR(255) NOT NULL, -- label or GO ID
secondary CHAR(10) NULL, -- GO ID
like_go_id SMALLINT, -- boolean (1 or 0)
FOREIGN KEY (_id) REFERENCES go_term (_id)
);
CREATE TABLE go_bp_offspring (
_id INTEGER NOT NULL, -- REFERENCES go_term
_offspring_id INTEGER NOT NULL, -- REFERENCES go_term
FOREIGN KEY (_id) REFERENCES go_term (_id),
FOREIGN KEY (_offspring_id) REFERENCES go_term (_id)
);
CREATE TABLE go_mf_offspring (
_id INTEGER NOT NULL, -- REFERENCES go_term
_offspring_id INTEGER NOT NULL, -- REFERENCES go_term
FOREIGN KEY (_id) REFERENCES go_term (_id),
FOREIGN KEY (_offspring_id) REFERENCES go_term (_id)
);
CREATE TABLE go_cc_offspring (
_id INTEGER NOT NULL, -- REFERENCES go_term
_offspring_id INTEGER NOT NULL, -- REFERENCES go_term
FOREIGN KEY (_id) REFERENCES go_term (_id),
FOREIGN KEY (_offspring_id) REFERENCES go_term (_id)
);
CREATE TABLE go_bp_parents (
_id INTEGER NOT NULL, -- REFERENCES go_term
_parent_id INTEGER NOT NULL, -- REFERENCES go_term
relationship_type VARCHAR(7) NOT NULL, -- type of GO child-parent relationship
FOREIGN KEY (_id) REFERENCES go_term (_id),
FOREIGN KEY (_parent_id) REFERENCES go_term (_id)
);
CREATE TABLE go_mf_parents (
_id INTEGER NOT NULL, -- REFERENCES go_term
_parent_id INTEGER NOT NULL, -- REFERENCES go_term
relationship_type VARCHAR(7) NOT NULL, -- type of GO child-parent relationship
FOREIGN KEY (_id) REFERENCES go_term (_id),
FOREIGN KEY (_parent_id) REFERENCES go_term (_id)
);
CREATE TABLE go_cc_parents (
_id INTEGER NOT NULL, -- REFERENCES go_term
_parent_id INTEGER NOT NULL, -- REFERENCES go_term
relationship_type VARCHAR(7) NOT NULL, -- type of GO child-parent relationship
FOREIGN KEY (_id) REFERENCES go_term (_id),
FOREIGN KEY (_parent_id) REFERENCES go_term (_id)
);
CREATE TABLE map_metadata (
map_name VARCHAR(80) NOT NULL,
source_name VARCHAR(80) NOT NULL,
source_url VARCHAR(255) NOT NULL,
source_date VARCHAR(20) NOT NULL
);
CREATE TABLE map_counts (
map_name VARCHAR(80) PRIMARY KEY,
count INTEGER NOT NULL
);
-- Explicit index creation on the referencing column of all the foreign keys.
-- Note that this is only needed for SQLite: PostgreSQL and MySQL create those
-- indexes automatically.
CREATE INDEX Fgo_term ON go_term (ontology);
CREATE INDEX Fgo_obsolete ON go_obsolete (ontology);
CREATE INDEX gs2 on go_synonym(synonym);
CREATE INDEX Fgo_synonym ON go_synonym (_id);
CREATE INDEX of1 on go_bp_offspring(_id, _offspring_id);
CREATE INDEX of2 on go_bp_offspring(_offspring_id, _id);
CREATE INDEX F1go_bp_offspring ON go_bp_offspring (_id);
CREATE INDEX F2go_bp_offspring ON go_bp_offspring (_offspring_id);
CREATE INDEX of3 on go_mf_offspring(_id, _offspring_id);
CREATE INDEX of4 on go_mf_offspring(_offspring_id, _id);
CREATE INDEX F1go_mf_offspring ON go_mf_offspring (_id);
CREATE INDEX F2go_mf_offspring ON go_mf_offspring (_offspring_id);
CREATE INDEX of5 on go_cc_offspring(_id, _offspring_id);
CREATE INDEX of6 on go_cc_offspring(_offspring_id, _id);
CREATE INDEX F1go_cc_offspring ON go_cc_offspring (_id);
CREATE INDEX F2go_cc_offspring ON go_cc_offspring (_offspring_id);
CREATE INDEX pa1 on go_bp_parents(_id, _parent_id);
CREATE INDEX pa2 on go_bp_parents(_parent_id, _id);
CREATE INDEX F1go_bp_parents ON go_bp_parents (_id);
CREATE INDEX F2go_bp_parents ON go_bp_parents (_parent_id);
CREATE INDEX pa3 on go_mf_parents(_id, _parent_id);
CREATE INDEX pa4 on go_mf_parents(_parent_id, _id);
CREATE INDEX F1go_mf_parents ON go_mf_parents (_id);
CREATE INDEX F2go_mf_parents ON go_mf_parents (_parent_id);
CREATE INDEX pa5 on go_cc_parents(_id, _parent_id);
CREATE INDEX pa6 on go_cc_parents(_parent_id, _id);
CREATE INDEX F1go_cc_parents ON go_cc_parents (_id);
CREATE INDEX F2go_cc_parents ON go_cc_parents (_parent_id);
|