/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_0.9/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 | --
-- YEAST_DB schema
-- ===============
--
-- The "sgd" table is the central table.
CREATE TABLE sgd (
id INTEGER PRIMARY KEY,
systematic_name VARCHAR(14) NULL UNIQUE, -- Yeast ORF ID
gene_name VARCHAR(14) NULL UNIQUE, -- Yeast gene name
sgd_id CHAR(10) NOT NULL UNIQUE -- SGD ID
);
-- Data linked to the "sgd" table.
CREATE TABLE chromosome_features (
id INTEGER NOT NULL, -- REFERENCES sgd
chromosome VARCHAR(2) NULL, -- chromosome name
start INTEGER NULL,
feature_description TEXT NULL, -- Yeast feature description
FOREIGN KEY (id) REFERENCES sgd (id)
);
CREATE TABLE ec (
id INTEGER NOT NULL, -- REFERENCES sgd
ec_number VARCHAR(13) NOT NULL, -- EC number (no "EC:" prefix)
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 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_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_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_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 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_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 interpro (
id INTEGER NOT NULL, -- REFERENCES sgd
interpro_id CHAR(9) NOT NULL, -- InterPro ID
FOREIGN KEY (id) REFERENCES sgd (id)
);
CREATE TABLE kegg (
id INTEGER NOT NULL, -- REFERENCES sgd
kegg_id CHAR(5) NOT NULL, -- KEGG pathway short ID
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 pubmed (
id INTEGER NOT NULL, -- REFERENCES sgd
pubmed_id VARCHAR(10) NOT NULL, -- PubMed 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)
);
-- Standalone data tables.
CREATE TABLE chrlengths (
chr VARCHAR(2) PRIMARY KEY, -- chromosome name
length INTEGER NOT NULL
);
CREATE TABLE gene2systematic (
gene_name VARCHAR(14) NULL, -- Yeast gene name
systematic_name VARCHAR(14) NULL -- Yeast ORF ID
);
CREATE TABLE reject_orf (
systematic_name VARCHAR(14) PRIMARY KEY -- Yeast ORF ID
);
-- Metadata tables.
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
CREATE TABLE qcdata (
map_name VARCHAR(80) PRIMARY KEY,
count INTEGER NOT NULL
);
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
);
-- 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 Fec ON ec (id);
CREATE INDEX Fgene2alias ON gene2alias (id);
CREATE INDEX Fgo_bp ON go_bp (id);
CREATE INDEX Fgo_bp_all ON go_bp_all (id);
CREATE INDEX Fgo_cc ON go_cc (id);
CREATE INDEX Fgo_cc_all ON go_cc_all (id);
CREATE INDEX Fgo_mf ON go_mf (id);
CREATE INDEX Fgo_mf_all ON go_mf_all (id);
CREATE INDEX Finterpro ON interpro (id);
CREATE INDEX Fkegg ON kegg (id);
CREATE INDEX Fpfam ON pfam (id);
CREATE INDEX Fpubmed ON pubmed (id);
CREATE INDEX Fsmart ON smart (id);
|