/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.1/COELICOLOR_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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 | CREATE TABLE gene_info (
_id INTEGER REFERENCES genes(_id),
gene_name TEXT,
symbol TEXT
);
CREATE TABLE refseq (
_id INTEGER REFERENCES genes(_id),
accession TEXT
);
CREATE TABLE ec (
_id INTEGER REFERENCES genes(_id),
ec_number TEXT
);
CREATE TABLE kegg (
_id INTEGER REFERENCES genes(_id),
path_id TEXT
);
CREATE TABLE map_metadata (
map_name TEXT,
source_name TEXT,
source_url TEXT,
source_date TEXT
);
CREATE TABLE pubmed (
_id INTEGER REFERENCES genes(_id),
pubmed_id TEXT
);
CREATE TABLE locus (
_id INTEGER REFERENCES genes(_id),
locus_tag TEXT -- SCO IDs
);
CREATE TABLE genes (
_id INTEGER PRIMARY KEY,
gene_id TEXT -- Entrez_Gene IDs
);
CREATE TABLE accessions (
_id INTEGER NOT NULL,
accession TEXT, -- RefSeq accessions
FOREIGN KEY (_id) REFERENCES genes(_id)
);
CREATE TABLE protein (
_id INTEGER REFERENCES genes(_id),
protein_gi TEXT
);
CREATE TABLE chrlengths (
chromosome VARCHAR(1) PRIMARY KEY, -- chromosome name [0: chromosome, 1: plasmid SCP1, 2: plasmid SCP2]
length INTEGER NOT NULL
);
CREATE TABLE chromosomes (
_id INTEGER NOT NULL, -- REFERENCES genes
chromosome VARCHAR(1), -- chromosome name
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE alias (
_id INTEGER NOT NULL, -- REFERENCES genes
alias_symbol VARCHAR(80) NOT NULL, -- gene symbol or alias (synonyms)
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
CREATE TABLE go_bp (
_id INTEGER REFERENCES genes(_id),
go_id TEXT,
evidence TEXT
);
CREATE TABLE go_cc (
_id INTEGER REFERENCES genes(_id),
go_id TEXT,
evidence TEXT
);
CREATE TABLE go_mf (
_id INTEGER REFERENCES genes(_id),
go_id TEXT,
evidence TEXT
);
CREATE TABLE go_bp_all (_id INTEGER REFERENCES genes(_id),go_id TEXT,evidence TEXT);
CREATE TABLE go_cc_all (_id INTEGER REFERENCES genes(_id),go_id TEXT,evidence TEXT);
CREATE TABLE go_mf_all (_id INTEGER REFERENCES genes(_id),go_id TEXT,evidence TEXT);
CREATE TABLE map_counts (
map_name VARCHAR(80) PRIMARY KEY,
count INTEGER NOT NULL
);
CREATE TABLE chromosome_locations (
_id INTEGER NOT NULL, -- REFERENCES genes
seqname VARCHAR(20) NOT NULL, -- chromosome name
start_location INTEGER NOT NULL,
end_location INTEGER NOT NULL,
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE symbol (
_id INTEGER REFERENCES genes(_id),
symbol TEXT
);
-- 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 en1 ON ec(_id);
CREATE INDEX gi1 ON gene_info(_id);
CREATE INDEX k1 ON kegg(_id);
CREATE INDEX pu1 ON pubmed(_id);
CREATE INDEX rs1 on refseq(_id);
CREATE INDEX lt1 ON locus(_id);
CREATE INDEX lt2 ON locus(locus_tag);
CREATE INDEX ge2 ON genes(gene_id);
CREATE INDEX ge1 on genes(_id);
CREATE INDEX ac1 ON accessions(_id);
CREATE INDEX ac2 ON accessions(accession);
CREATE INDEX pr1 ON protein(_id);
CREATE INDEX al1 ON alias(_id);
CREATE INDEX ch ON chromosomes (_id);
CREATE INDEX go1 ON go_bp(_id);
CREATE INDEX go2 ON go_mf(_id);
CREATE INDEX go3 ON go_cc(_id);
CREATE INDEX go4 ON go_bp(go_id);
CREATE INDEX go5 ON go_mf(go_id);
CREATE INDEX go6 ON go_cc(go_id);
CREATE INDEX chl ON chromosome_locations (_id);
CREATE INDEX gisymbol ON symbol(_id);
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