/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.0/ARABIDOPSIS_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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 | CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );
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
);
CREATE TABLE genes (
_id INTEGER PRIMARY KEY,
gene_id CHAR(9) NOT NULL UNIQUE -- AGI locus ID
);
CREATE TABLE sqlite_stat1(tbl,idx,stat);
CREATE TABLE entrez_genes (
_id INTEGER PRIMARY KEY,
gene_id CHAR(9) NOT NULL UNIQUE -- AGI locus ID
);
CREATE TABLE gene_info (
_id INTEGER NOT NULL, -- REFERENCES genes
gene_name VARCHAR(255) NULL, -- gene name
symbol VARCHAR(80) NULL, -- gene symbol
chromosome CHAR(1) NULL, -- Arabidopsis chromosome
FOREIGN KEY (_id) REFERENCES genes (_id));
CREATE TABLE pubmed (
_id INTEGER NOT NULL, -- REFERENCES genes
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE chrlengths (
chromosome VARCHAR(2) PRIMARY KEY, -- chromosome name
length INTEGER NOT NULL
);
CREATE TABLE go_bp (
_id INTEGER NOT NULL, -- REFERENCES genes
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE go_mf (
_id INTEGER NOT NULL, -- REFERENCES genes
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE go_cc (
_id INTEGER NOT NULL, -- REFERENCES genes
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE go_bp_all (
_id INTEGER NOT NULL, -- REFERENCES genes
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE go_mf_all (
_id INTEGER NOT NULL, -- REFERENCES genes
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE go_cc_all (
_id INTEGER NOT NULL, -- REFERENCES genes
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE kegg (
_id INTEGER NOT NULL, -- REFERENCES genes
path_id CHAR(5) NOT NULL, -- KEGG pathway short ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE ec (
_id INTEGER NOT NULL, -- REFERENCES genes
ec_number VARCHAR(13) NOT NULL, -- EC number
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE chromosome_locations (
_id INTEGER NOT NULL, -- REFERENCES genes
seqname VARCHAR(20) NOT NULL, -- sequence name
start_location INTEGER NOT NULL,
end_location INTEGER NOT NULL,
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE refseq (
_id INTEGER NOT NULL, -- REFERENCES genes
accession VARCHAR(20) NOT NULL, -- RefSeq accession number
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE aracyc (
_id INTEGER NOT NULL, -- REFERENCES genes
pathway_name VARCHAR(255) NOT NULL, -- AraCyc pathway name
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE enzyme (
_id INTEGER NOT NULL, -- REFERENCES genes
ec_name VARCHAR(255) NOT NULL, -- EC name
FOREIGN KEY (_id) REFERENCES genes (_id)
);
-- 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 Fentrez_genes ON entrez_genes(gene_id);
CREATE INDEX Fgene_info ON gene_info (_id);
CREATE INDEX Fpubmed ON pubmed (_id);
CREATE INDEX Fgo_bp ON go_bp (_id);
CREATE INDEX Fgo_bp_go_id ON go_bp (go_id);
CREATE INDEX Fgo_mf ON go_mf (_id);
CREATE INDEX Fgo_mf_go_id ON go_mf (go_id);
CREATE INDEX Fgo_cc ON go_cc (_id);
CREATE INDEX Fgo_cc_go_id ON go_cc (go_id);
CREATE INDEX Fgo_bp_all ON go_bp_all (_id);
CREATE INDEX Fgo_bp_all_go_id ON go_bp_all (go_id);
CREATE INDEX Fgo_mf_all ON go_mf_all (_id);
CREATE INDEX Fgo_mf_all_go_id ON go_mf_all (go_id);
CREATE INDEX Fgo_cc_all ON go_cc_all (_id);
CREATE INDEX Fgo_cc_all_go_id ON go_cc_all (go_id);
CREATE INDEX Fkegg ON kegg (_id);
CREATE INDEX Fec ON ec (_id);
CREATE INDEX Fchromosome_locations ON chromosome_locations (_id);
CREATE INDEX Frefseq ON refseq (_id);
CREATE INDEX Faracyc ON aracyc (_id);
CREATE INDEX Fenzyme ON enzyme (_id);
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