/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.1/YEAST_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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 | 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 sgd (
_id INTEGER PRIMARY KEY,
systematic_name VARCHAR(14) NULL UNIQUE, -- Yeast gene systematic name
gene_name VARCHAR(14) NULL UNIQUE, -- Yeast gene name
sgd_id CHAR(10) NOT NULL UNIQUE -- SGD ID
);
CREATE TABLE sqlite_stat1(tbl,idx,stat);
CREATE TABLE chromosome_features (
_id INTEGER NOT NULL, -- REFERENCES sgd
chromosome VARCHAR(2) NULL, -- chromosome name
start INTEGER NULL,
stop INTEGER NULL,
feature_description TEXT NULL, -- Yeast feature description
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE gene2alias (
_id INTEGER NOT NULL, -- REFERENCES sgd
alias VARCHAR(13) NOT NULL, -- Yeast gene alias
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE pubmed (
_id INTEGER NOT NULL, -- REFERENCES sgd
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE chrlengths (
chromosome VARCHAR(2) PRIMARY KEY, -- chromosome name
length INTEGER NOT NULL
);
CREATE TABLE go_bp (
_id INTEGER NOT NULL, -- REFERENCES sgd
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE go_mf (
_id INTEGER NOT NULL, -- REFERENCES sgd
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE go_cc (
_id INTEGER NOT NULL, -- REFERENCES sgd
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE go_bp_all (
_id INTEGER NOT NULL, -- REFERENCES sgd
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE go_mf_all (
_id INTEGER NOT NULL, -- REFERENCES sgd
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE go_cc_all (
_id INTEGER NOT NULL, -- REFERENCES sgd
go_id CHAR(10) NOT NULL, -- GO ID
evidence CHAR(3) NOT NULL, -- GO evidence code
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE kegg (
_id INTEGER NOT NULL, -- REFERENCES sgd
path_id CHAR(5) NOT NULL, -- KEGG pathway short ID
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE ec (
_id INTEGER NOT NULL, -- REFERENCES sgd
ec_number VARCHAR(13) NOT NULL, -- EC number
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE pfam (
_id INTEGER NOT NULL, -- REFERENCES sgd
pfam_id CHAR(7) NOT NULL, -- Pfam ID
FOREIGN KEY (_id) REFERENCES sgd (_id));
CREATE TABLE smart (
_id INTEGER NOT NULL, -- REFERENCES sgd
smart_id CHAR(7) NOT NULL, -- SMART ID
FOREIGN KEY (_id) REFERENCES sgd (_id));
CREATE TABLE interpro (
_id INTEGER NOT NULL, -- REFERENCES sgd
interpro_id CHAR(9) NOT NULL, -- InterPro ID
FOREIGN KEY (_id) REFERENCES sgd (_id));
CREATE TABLE reject_orf (
systematic_name VARCHAR(14) PRIMARY KEY);
CREATE TABLE gene2systematic (
gene_name VARCHAR(14) NULL, -- Yeast gene name
systematic_name VARCHAR(14) NULL);
CREATE TABLE genes (
_id INTEGER NOT NULL, -- REFERENCES sgd
gene_id VARCHAR(20) NOT NULL, -- gene id
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE ensembl (
_id INTEGER NOT NULL, -- REFERENCES sgd
ensembl_id VARCHAR(20) NOT NULL, -- ensembl id
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE ensembl2ncbi (
_id INTEGER NOT NULL, -- REFERENCES sgd
ensembl_id VARCHAR(20) NOT NULL, -- ensembl id
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE ncbi2ensembl (
_id INTEGER NOT NULL, -- REFERENCES sgd
ensembl_id VARCHAR(20) NOT NULL, -- ensembl id
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE ensembl_prot (
_id INTEGER NOT NULL, -- REFERENCES sgd
prot_id VARCHAR(20) NOT NULL, -- Ensembl Protein ID
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE ensembl_trans (
_id INTEGER NOT NULL, -- REFERENCES sgd
trans_id VARCHAR(20) NOT NULL, -- Ensembl Transcript ID
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE uniprot (
_id INTEGER NOT NULL, -- REFERENCES sgd
uniprot_id VARCHAR(20) NOT NULL, -- uniprot id
FOREIGN KEY (_id) REFERENCES sgd (_id)
);
CREATE TABLE refseq (
_id INTEGER NOT NULL, -- REFERENCES sgd
accession VARCHAR(20) NOT NULL, -- RefSeq accession number
FOREIGN KEY (_id) REFERENCES sgd (_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 Fchromosome_features ON chromosome_features (_id);
CREATE INDEX Fgene2alias ON gene2alias(_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 Fpfam ON pfam (_id);
CREATE INDEX Fsmart ON smart (_id);
CREATE INDEX Finterpro ON interpro (_id);
CREATE INDEX Fgene ON genes(_id);
CREATE INDEX Fensembl ON ensembl (_id);
CREATE INDEX Fensembl2ncbi ON ensembl2ncbi (_id);
CREATE INDEX Fncbi2ensembl ON ncbi2ensembl (_id);
CREATE INDEX Fensemblp ON ensembl_prot (_id);
CREATE INDEX Fensemblt ON ensembl_trans (_id);
CREATE INDEX Funiprot ON uniprot (_id);
CREATE INDEX Frefseq ON refseq (_id);
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