--
-- RATCHIP_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 probes (
  probe_id VARCHAR(80) PRIMARY KEY,             -- manufacturer ID
  accession VARCHAR(20) NULL,                   -- GenBank accession number
  _id INTEGER NULL,                             -- REFERENCES genes
  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 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 cytogenetic_locations (
  _id INTEGER NOT NULL,                         -- REFERENCES genes
  cytogenetic_location VARCHAR(20) NOT NULL,    -- cytoband location
  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 Fprobes ON probes (_id);
CREATE INDEX Falias ON alias (_id);
CREATE INDEX Fchromosomes ON chromosomes (_id);
CREATE INDEX Fchromosome_locations ON chromosome_locations (_id);
CREATE INDEX Fcytogenetic_locations ON cytogenetic_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);

