/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_1.0/CHICKEN_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.
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-- CHICKEN_DB schema
-- ===============
--
-- The "genes" table is the central table.
CREATE TABLE genes (
_id INTEGER PRIMARY KEY,
gene_id VARCHAR(10) NOT NULL UNIQUE -- Entrez Gene ID
);
-- Data linked to the "genes" table.
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 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 ensembl (
_id INTEGER NOT NULL, -- REFERENCES genes
ensembl_id VARCHAR(20) NOT NULL, -- Ensembl Gene ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE ensembl_prot (
_id INTEGER NOT NULL, -- REFERENCES genes
prot_id VARCHAR(20) NOT NULL, -- Ensembl Protein ID
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 chromosome_locations (
_id INTEGER NOT NULL, -- REFERENCES genes
seqname VARCHAR(20) NOT NULL, -- sequence name
start_location INTEGER NOT NULL,
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE ec (
_id INTEGER NOT NULL, -- REFERENCES genes
ec_number VARCHAR(13) NOT NULL, -- EC number (no "EC:" prefix)
FOREIGN KEY (_id) REFERENCES genes (_id)
);
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 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_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_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_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 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_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 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 pfam (
_id INTEGER NOT NULL, -- REFERENCES genes
ipi_id CHAR(11) NOT NULL, -- IPI accession number
pfam_id CHAR(7) NULL, -- Pfam ID
FOREIGN KEY (_id) REFERENCES genes (_id)
);
CREATE TABLE prosite (
_id INTEGER NOT NULL, -- REFERENCES genes
ipi_id CHAR(11) NOT NULL, -- IPI accession number
prosite_id CHAR(7) NULL, -- PROSITE ID
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 refseq (
_id INTEGER NOT NULL, -- REFERENCES genes
accession VARCHAR(20) NOT NULL, -- RefSeq accession number
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)
);
-- Standalone data tables.
CREATE TABLE chrlengths (
chromosome VARCHAR(2) PRIMARY KEY, -- chromosome name
length INTEGER NOT NULL
);
-- Metadata tables.
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
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 Faccessions ON accessions (_id);
CREATE INDEX Falias ON alias (_id);
CREATE INDEX Fchromosomes ON chromosomes (_id);
CREATE INDEX Fchromosome_locations ON chromosome_locations (_id);
CREATE INDEX Fec ON ec (_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 Fkegg ON kegg (_id);
CREATE INDEX Fpfam ON pfam (_id);
CREATE INDEX Fprosite ON prosite (_id);
CREATE INDEX Fpubmed ON pubmed (_id);
CREATE INDEX Frefseq ON refseq (_id);
CREATE INDEX Funigene ON unigene (_id);
CREATE INDEX Fensembl ON ensembl (_id);
CREATE INDEX Fensemblp ON ensembl_prot (_id);
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