/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_2.1/PFAM_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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name TEXT,
value TEXT
);
CREATE TABLE cazy (
ac VARCHAR(12) NOT NULL, --AC ID
cazy VARCHAR(6) NOT NULL --CAZY ID
);
CREATE TABLE homstrad (
ac VARCHAR(12) NOT NULL, --AC ID
homstrad VARCHAR(20) NOT NULL --HOMSTRAD ID
);
CREATE TABLE interpro (
ac VARCHAR(12) NOT NULL, --AC ID
interpro VARCHAR(9) NOT NULL --INTERPRO ID
);
CREATE TABLE load (
ac VARCHAR(12) NOT NULL, --AC ID
load VARCHAR(15) NOT NULL --LOAD ID
);
CREATE TABLE merops (
ac VARCHAR(12) NOT NULL, --AC ID
merops VARCHAR(3) NOT NULL --MEROPS ID
);
CREATE TABLE mim (
ac VARCHAR(12) NOT NULL, --AC ID
mim VARCHAR(6) NOT NULL --MIM ID
);
CREATE TABLE pdb (
ac VARCHAR(12) NOT NULL, --AC ID
pdb VARCHAR(6) NOT NULL, --PDB ID
start_point INTEGER, --start of alignment
end_point INTEGER --end of alignment
);
CREATE TABLE prints (
ac VARCHAR(12) NOT NULL, --AC ID
prints VARCHAR(7) NOT NULL --PRINTS ID
);
CREATE TABLE prosite (
ac VARCHAR(12) NOT NULL, --AC ID
prosite VARCHAR(9) NOT NULL --PROSITE ID
);
CREATE TABLE prosite_profile (
ac VARCHAR(12) NOT NULL, --AC ID
prosite_profile VARCHAR(7) NOT NULL --PROSITE_PROFILE ID
);
CREATE TABLE rm (
ac VARCHAR(12) NOT NULL, --AC ID
rm VARCHAR(8) NOT NULL --RM ID
);
CREATE TABLE scop (
ac VARCHAR(12) NOT NULL, --AC ID
scop VARCHAR(4) NOT NULL, --SCOP ID
placement VARCHAR(2) NOT NULL --SCOP placement
);
CREATE TABLE smart (
ac VARCHAR(12) NOT NULL, --AC ID
smart VARCHAR(9) NOT NULL --SMART ID
);
CREATE TABLE tc (
ac VARCHAR(12) NOT NULL, --AC ID
tc VARCHAR(6) NOT NULL --TC ID
);
CREATE TABLE url (
ac VARCHAR(12) NOT NULL, --AC ID
url VARCHAR(80) NOT NULL --URL ID
);
CREATE TABLE id (
ac VARCHAR(12) NOT NULL, --AC ID
id VARCHAR(15) NOT NULL --ID ID
);
CREATE TABLE de (
ac VARCHAR(12) NOT NULL, --AC ID
de VARCHAR(80) NOT NULL --DE ID
);
CREATE TABLE tp (
ac VARCHAR(12) NOT NULL, --AC ID
tp VARCHAR(6) NOT NULL --TP ID
);
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 sqlite_stat1(tbl,idx,stat);
-- 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 cazy_ac ON cazy(ac);
CREATE INDEX homstrad_ac ON homstrad(ac);
CREATE INDEX interpro_ac ON interpro(ac);
CREATE INDEX load_ac ON load(ac);
CREATE INDEX merops_ac ON merops(ac);
CREATE INDEX mim_ac ON mim(ac);
CREATE INDEX pdb_ac ON pdb(ac);
CREATE INDEX prints_ac ON prints(ac);
CREATE INDEX prosite_ac ON prosite(ac);
CREATE INDEX prosite_profile_ac ON prosite_profile(ac);
CREATE INDEX rm_ac ON rm(ac);
CREATE INDEX scop_ac ON scop(ac);
CREATE INDEX smart_ac ON smart(ac);
CREATE INDEX tc_ac ON tc(ac);
CREATE INDEX url_ac ON url(ac);
CREATE INDEX id_ac ON id(ac);
CREATE INDEX de_ac ON de(ac);
CREATE INDEX tp_ac ON tp(ac);
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