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Revision 1.4 - (download) (annotate)
Thu Apr 5 15:29:12 2007 UTC (12 years, 8 months ago) by bartels
Branch: MAIN
CVS Tags: HEAD
Changes since 1.3: +32 -5 lines
*** empty log message ***

CREATE DATABASE GBBergeyDB;
USE GBBergeyDB;
CREATE TABLE _metainfo (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id), info_name CHAR(255), info_value CHAR(255));
CREATE TABLE _references (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id), _database CHAR(255));
INSERT INTO _metainfo (info_name, info_value) VALUES('module_name', 'GBBergeyDB');
CREATE TABLE _objects (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id), object CHAR(255));
INSERT INTO _objects (object) VALUES ('Contact');
CREATE TABLE Contact (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	email CHAR(250),
	url CHAR(250),
	name CHAR(250)
	);
CREATE TABLE Genome_strainAliases (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	_array_index int,
	_source_id int,
	_value CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('GOrder');
CREATE TABLE GOrder (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	taxDOI INT,
	name CHAR(250),
	Class int,
	_Class_db int
	);
INSERT INTO _objects (object) VALUES ('GenomeAlias');
CREATE TABLE GenomeAlias (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	aliasType CHAR(250),
	name CHAR(250),
	ident INT,
	taxid INT,
	scientificName CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('GenomeDatabase');
CREATE TABLE GenomeDatabase (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	url CHAR(250),
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Publication');
CREATE TABLE Publication (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	number INT,
	url CHAR(250),
	pages CHAR(250),
	journal CHAR(250),
	year INT,
	pubmed INT
	);
CREATE TABLE GenomeSequence_FundingOrganisation (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	_array_index int,
	_target_id int,
	_source_id int,
	_target_db int
	);
INSERT INTO _objects (object) VALUES ('Family');
CREATE TABLE Family (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	GOrder int,
	_GOrder_db int,
	taxDOI INT,
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('SOP');
CREATE TABLE SOP (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	date DATE,
	url CHAR(255),
	name CHAR(50),
	note TEXT
	);
CREATE UNIQUE INDEX SOP_name_date_key ON SOP (name, date);
INSERT INTO _objects (object) VALUES ('GenomeFeatures');
CREATE TABLE GenomeFeatures (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	value CHAR(250),
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Species');
CREATE TABLE Species (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	userflag4 INT,
	userflag3 INT,
	computedscore INT,
	added INT,
	name CHAR(250),
	score INT,
	ScientificSpecies int,
	_ScientificSpecies_db int,
	taxid INT,
	litNum INT,
	userflag1 INT,
	taxDOI INT,
	Genus int,
	_Genus_db int,
	userflag2 INT
	);
INSERT INTO _objects (object) VALUES ('File');
CREATE TABLE File (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	file_type VARCHAR(25),
	uid text,
	name VARCHAR(255),
	creation_time int,
	sequence_type CHAR(25),
	path VARCHAR(255)
	);
CREATE UNIQUE INDEX File_name_path_creation_time_key ON File (name, path, creation_time);
CREATE TABLE GenomeSequence_GenomeDatabase (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	_array_index int,
	_target_id int,
	_source_id int,
	_target_db int
	);
INSERT INTO _objects (object) VALUES ('SequenceLog');
CREATE TABLE SequenceLog (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	sequence int,
	_sequence_db int,
	date int,
	organism int,
	_organism_db int,
	event CHAR(255),
	note CHAR(255)
	);
CREATE TABLE Species_litArray (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	_array_index int,
	_source_id int,
	_value CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('STScluster');
CREATE TABLE STScluster (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	litCount INT,
	number INT,
	representative2 int,
	_representative2_db int,
	representative int,
	_representative_db int,
	score FLOAT,
	seqrepresentation INT
	);
CREATE TABLE Genome_addFeatures (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	_array_index int,
	_source_id int,
	_value CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Genome');
CREATE TABLE Genome (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	inList INT,
	collectionStatus CHAR(250),
	InSEED INT,
	taxid CHAR(16),
	prokMSAname CHAR(250),
	exemplarDOI INT,
	taxonDOI INT,
	InGenomeData INT,
	InGOLD INT,
	STSvalue FLOAT,
	obligate CHAR(125),
	ncbiNumber INT,
	CMRAlias CHAR(125),
	temperature INT,
	carbon CHAR(250),
	hxh INT,
	extremophile CHAR(250),
	name CHAR(250),
	orderOfPublication INT,
	ncNumber CHAR(125),
	RDPID INT,
	InSTS INT,
	motile CHAR(125),
	cultivationStatus CHAR(255),
	typeStrain INT,
	desease INT,
	genetic_code CHAR(255),
	shape CHAR(125),
	InCCUG INT,
	JGIStatus CHAR(250),
	width FLOAT,
	energy CHAR(250),
	pH FLOAT,
	doubleTimeMins INT,
	gramStain CHAR(125),
	oxygen CHAR(250),
	nameDOI CHAR(250),
	Species int,
	_Species_db int,
	habitat CHAR(250),
	sixTeenS TEXT,
	InNCBI INT,
	numberChromosomes INT,
	STScluster int,
	_STScluster_db int,
	goldstamp CHAR(125),
	chromosomeType CHAR(250),
	estiGenomeSize INT,
	InDSMZ INT,
	CMRID INT,
	totalReplicons INT,
	genBank CHAR(250),
	figid CHAR(16),
	sequencingStatus CHAR(250),
	InBergey INT,
	prokMSAid INT
	);
INSERT INTO _objects (object) VALUES ('Domain');
CREATE TABLE Domain (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	taxDOI INT,
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Phyla');
CREATE TABLE Phyla (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	taxDOI INT,
	Domain int,
	_Domain_db int,
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Note');
CREATE TABLE Note (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	Species int,
	_Species_db int,
	timestamp INT,
	user CHAR(250),
	Strain int,
	_Strain_db int,
	confidence INT,
	description CHAR(250),
	voting INT
	);
INSERT INTO _objects (object) VALUES ('GenomeSequence');
CREATE TABLE GenomeSequence (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	Contact int,
	_Contact_db int,
	genecalling char(255),
	genecallingSop int,
	_genecallingSop_db int,
	genecallingDate int,
	project CHAR(255),
	Publication int,
	_Publication_db int,
	noORFs INT,
	sequenceSourceLink CHAR(255),
	releaseDate int,
	seedStatus CHAR(50),
	Genome int,
	_Genome_db int,
	version int,
	sequenceLength INT,
	sequenceFile int,
	_sequenceFile_db int,
	comment CHAR(255),
	lastUpdate char(255),
	insertionDate int,
	sequenceChecksum int,
	type char(50),
	sequenceQuality CHAR(255),
	seedID VARCHAR(255)
	);
CREATE TABLE GenomeSequence_Institution (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	_array_index int,
	_target_id int,
	_source_id int,
	_target_db int
	);
INSERT INTO _objects (object) VALUES ('Institution');
CREATE TABLE Institution (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	url CHAR(250),
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Genus');
CREATE TABLE Genus (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	taxDOI INT,
	Family int,
	_Family_db int,
	form INT,
	name CHAR(250)
	);
INSERT INTO _objects (object) VALUES ('Class');
CREATE TABLE Class (_id int NOT NULL AUTO_INCREMENT, PRIMARY KEY (_id),
	taxDOI INT,
	Phyla int,
	_Phyla_db int,
	name CHAR(250)
	);

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