/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.0/FLY_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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 | 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 VARCHAR(10) NOT NULL UNIQUE -- Entrez Gene ID
);
CREATE TABLE sqlite_stat1(tbl,idx,stat);
CREATE TABLE gene_info (
_id INTEGER NOT NULL UNIQUE, -- REFERENCES genes
gene_name VARCHAR(255) NOT NULL, -- gene name
symbol VARCHAR(80) NOT NULL, -- gene symbol
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE chromosomes (
_id INTEGER NOT NULL, -- REFERENCES genes
chromosome VARCHAR(2) NOT NULL, -- chromosome name
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE accessions (
_id INTEGER NOT NULL, -- REFERENCES genes
accession VARCHAR(20) NOT NULL, -- GenBank accession number
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE cytogenetic_locations (
_id INTEGER NOT NULL, -- REFERENCES genes
cytogenetic_location VARCHAR(20) NOT NULL, -- cytoband location
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 pubmed (
_id INTEGER NOT NULL, -- REFERENCES genes
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE unigene (
_id INTEGER NOT NULL, -- REFERENCES genes
unigene_id VARCHAR(10) NOT NULL, -- UniGene 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 alias (
_id INTEGER NOT NULL, -- REFERENCES genes
alias_symbol VARCHAR(80) NOT NULL, -- gene symbol or alias
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE uniprot (
_id INTEGER NOT NULL, -- REFERENCES genes
uniprot_id VARCHAR(20) NOT NULL, -- uniprot id
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE flybase (
_id INTEGER NOT NULL, -- REFERENCES genes
flybase_id VARCHAR(80) NOT NULL, -- FlyBase ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE flybase_cg (
_id INTEGER NOT NULL, -- REFERENCES genes
flybase_cg_id VARCHAR(10) NOT NULL, -- FlyBase CG ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE flybase_prot (
_id INTEGER NOT NULL, -- REFERENCES genes
prot_id VARCHAR(20) NOT NULL, -- Flybase Protein ID
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 Fchromosomes ON chromosomes (_id);
CREATE INDEX Faccessions ON accessions (_id);
CREATE INDEX Fcytogenetic_locations ON cytogenetic_locations (_id);
CREATE INDEX Frefseq ON refseq (_id);
CREATE INDEX Fpubmed ON pubmed (_id);
CREATE INDEX Funigene ON unigene (_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 Falias ON alias (_id);
CREATE INDEX Funiprot ON uniprot (_id);
CREATE INDEX Fflybase ON flybase (_id);
CREATE INDEX Fflybasecg ON flybase_cg (_id);
CREATE INDEX Fflybasep ON flybase_prot (_id);
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