/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.1/KEGG_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 | CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
CREATE TABLE pathway2name (
path_id CHAR(5) NOT NULL UNIQUE, -- KEGG pathway short ID
path_name VARCHAR(100) NOT NULL UNIQUE -- KEGG pathway name
);
CREATE TABLE pathway2gene (
pathway_id CHAR(8) NOT NULL, -- KEGG pathway long ID
gene_or_orf_id VARCHAR(20) NOT NULL -- Entrez Gene or ORF ID
);
CREATE TABLE ath_NCBI_pathway2gene (
pathway_id CHAR(8) NOT NULL, -- KEGG pathway long ID
gene_or_orf_id VARCHAR(20) NOT NULL -- Entrez Gene or ORF ID
);
CREATE TABLE ec2go(ec_no VARCHAR(16),go_id CHAR(10));
CREATE TABLE map_counts (
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 Ipathway2gene ON pathway2gene (gene_or_orf_id);
CREATE INDEX ath_NCBI_Ipathway2gene ON ath_NCBI_pathway2gene (gene_or_orf_id);
|