/usr/lib/R/site-library/AnnotationDbi/DBschemas/schemas_1.0/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.
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 | CREATE TABLE metadata (
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 pfamb (
ac VARCHAR(12) NOT NULL, --AC ID
pfamb VARCHAR(8) NOT NULL --PFAMB ID
);
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 --PFAM 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
);
-- 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 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 pfamb_ac ON pfamb(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);
|