--- biosqldb-pg.sql.original 2007-10-21 21:51:31.000000000 +0200 +++ biosqldb-pg.sql 2007-10-21 22:05:14.000000000 +0200 @@ -42,8 +42,8 @@ CREATE SEQUENCE biodatabase_pk_seq; CREATE TABLE biodatabase ( biodatabase_id INTEGER DEFAULT nextval ( 'biodatabase_pk_seq' ) NOT NULL , - name VARCHAR ( 128 ) NOT NULL , - authority VARCHAR ( 128 ) , + name TEXT NOT NULL , + authority TEXT , description TEXT , PRIMARY KEY ( biodatabase_id ) , UNIQUE ( name ) ) ; @@ -64,7 +64,7 @@ taxon_id INTEGER DEFAULT nextval ( 'taxon_pk_seq' ) NOT NULL , ncbi_taxon_id INTEGER , parent_taxon_id INTEGER , - node_rank VARCHAR ( 32 ) , + node_rank TEXT , genetic_code SMALLINT , mito_genetic_code SMALLINT , left_value INTEGER , @@ -79,8 +79,8 @@ -- corresponds to the names table of the NCBI taxonomy databaase CREATE TABLE taxon_name ( taxon_id INTEGER NOT NULL , - name VARCHAR ( 255 ) NOT NULL , - name_class VARCHAR ( 32 ) NOT NULL , + name TEXT NOT NULL , + name_class TEXT NOT NULL , UNIQUE ( name , name_class, taxon_id ) ) ; CREATE INDEX taxnametaxonid ON taxon_name ( taxon_id ); @@ -91,7 +91,7 @@ CREATE SEQUENCE ontology_pk_seq; CREATE TABLE ontology ( ontology_id INTEGER DEFAULT nextval ( 'ontology_pk_seq' ) NOT NULL , - name VARCHAR ( 32 ) NOT NULL , + name TEXT NOT NULL , definition TEXT , PRIMARY KEY ( ontology_id ) , UNIQUE ( name ) ) ; @@ -101,9 +101,9 @@ CREATE SEQUENCE term_pk_seq; CREATE TABLE term ( term_id INTEGER DEFAULT nextval ( 'term_pk_seq' ) NOT NULL , - name VARCHAR ( 255 ) NOT NULL , + name TEXT NOT NULL , definition TEXT , - identifier VARCHAR ( 40 ) , + identifier TEXT , is_obsolete CHAR ( 1 ) , ontology_id INTEGER NOT NULL , PRIMARY KEY ( term_id ) , @@ -125,7 +125,7 @@ -- Synonym is a reserved word in many RDBMSs, so the column synonym -- may eventually be renamed to name. CREATE TABLE term_synonym ( - synonym VARCHAR(255) NOT NULL, + synonym TEXT NOT NULL, term_id INTEGER NOT NULL, PRIMARY KEY ( term_id , synonym ) ) ; @@ -236,10 +236,10 @@ bioentry_id INTEGER DEFAULT nextval ( 'bioentry_pk_seq' ) NOT NULL , biodatabase_id INTEGER NOT NULL , taxon_id INTEGER , - name VARCHAR ( 40 ) NOT NULL , - accession VARCHAR ( 40 ) NOT NULL , - identifier VARCHAR ( 40 ) , - division VARCHAR ( 6 ) , + name TEXT NOT NULL , + accession TEXT NOT NULL , + identifier TEXT , + division TEXT , description TEXT , version INTEGER NOT NULL , PRIMARY KEY ( bioentry_id ) , @@ -296,7 +296,7 @@ bioentry_id INTEGER NOT NULL , version INTEGER , length INTEGER , - alphabet VARCHAR ( 10 ) , + alphabet TEXT , seq TEXT , PRIMARY KEY ( bioentry_id ) ) ; @@ -317,8 +317,8 @@ CREATE SEQUENCE dbxref_pk_seq; CREATE TABLE dbxref ( dbxref_id INTEGER DEFAULT nextval ( 'dbxref_pk_seq' ) NOT NULL , - dbname VARCHAR ( 40 ) NOT NULL , - accession VARCHAR ( 40 ) NOT NULL , + dbname TEXT NOT NULL , + accession TEXT NOT NULL , version INTEGER NOT NULL , PRIMARY KEY ( dbxref_id ) , UNIQUE ( accession , dbname , version ) ) ; @@ -368,7 +368,7 @@ location TEXT NOT NULL , title TEXT , authors TEXT , - crc VARCHAR ( 32 ) , + crc TEXT , PRIMARY KEY ( reference_id ) , UNIQUE ( dbxref_id ) , UNIQUE ( crc ) ) ; @@ -415,7 +415,7 @@ bioentry_id INTEGER NOT NULL , type_term_id INTEGER NOT NULL , source_term_id INTEGER NOT NULL , - display_name VARCHAR ( 64 ) , + display_name TEXT , rank INTEGER NOT NULL DEFAULT 0 , PRIMARY KEY ( seqfeature_id ) , UNIQUE ( bioentry_id , type_term_id , source_term_id , rank ) ) ; @@ -525,7 +525,7 @@ CREATE TABLE location_qualifier_value ( location_id INTEGER NOT NULL , term_id INTEGER NOT NULL , - value VARCHAR ( 255 ) NOT NULL , + value TEXT NOT NULL , int_value INTEGER , PRIMARY KEY ( location_id , term_id ) ) ;