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Commit 1ec4047f authored by Monika Komorowska's avatar Monika Komorowska
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Moved new operon tables to the fundamental tables section.

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sql/table.sql
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− 125
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......@@ -515,6 +515,137 @@ CREATE TABLE meta_coord (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon
@desc allows one or more polycistronic transcripts to be grouped together
@column operon_id Primary key, internal identifier.
@column analysis_id Foreign key references to the @link analysis table.
@column seq_region_id Foreign key references to the @link seq_region table.
@column seq_region_start Sequence start position.
@column seq_region_end Sequence end position.
@column seq_region_strand Sequence region strand: 1 - forward; -1 - reverse.
@column display_label Short name for operon
@see operon_transcript
@see operon_stable_id
*/
CREATE TABLE operon (
operon_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT(2) NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
PRIMARY KEY (operon_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY name_idx (display_label)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_stable_id
@desc Relates operon IDs in this release to release-independent stable identifiers.
@column operon_id Primary key, internal identifier. Foreign key references to the @link operon table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see operon
*/
CREATE TABLE operon_stable_id (
operon_id INT UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (operon_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_transcript
@desc represents polycistronic transcripts which belong to operons and encode more than one gene
@column operon_transcript_id Primary key, internal identifier.
@column analysis_id Foreign key references to the @link analysis table.
@column seq_region_id Foreign key references to the @link seq_region table.
@column seq_region_start Sequence start position.
@column seq_region_end Sequence end position.
@column seq_region_strand Sequence region strand: 1 - forward; -1 - reverse.
@column operon_id Foreign key references to the @link operon table.
@column display_label Short name for operon transcript
@see operon
@see operon_transcript_stable_id
@see operon_transcript_gene
*/
CREATE TABLE operon_transcript (
operon_transcript_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT(2) NOT NULL,
operon_id INT(10) UNSIGNED NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
PRIMARY KEY (operon_transcript_id),
KEY operon_idx (operon_id),
KEY seq_region_idx (seq_region_id, seq_region_start)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_transcript_stable_id
@desc Relates operon polycistronic transcripts IDs in this release to release-independent stable identifiers.
@column operon_transcript_id Primary key, internal identifier. Foreign key references to the @link operon_transcript table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see operon_transcript
*/
CREATE TABLE operon_transcript_stable_id (
operon_transcript_id INT UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (operon_transcript_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_transcript_gene
@desc allows association of genes with polycistronic transcripts
@column operon_transcript_id Foreign key references to the @link operon_transcript table.
@column gene_id Foreign key references to the @link gene table.
@see operon_transcript
@see gene
*/
CREATE TABLE operon_transcript_gene (
operon_transcript_id INT(10) UNSIGNED,
gene_id INT(10) UNSIGNED,
KEY operon_transcript_gene_idx (operon_transcript_id,gene_id)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table seq_region
@desc Stores information about sequence regions. The primary key is used as a pointer into the dna table so that actual sequence can be obtained, and the coord_system_id allows sequence regions of multiple types to be stored.
......@@ -2470,128 +2601,3 @@ CREATE TABLE interpro (
KEY id_idx (id)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon
@desc allows one or more polycistronic transcripts to be grouped together
@column operon_id Primary key, internal identifier.
@column analysis_id Foreign key references to the @link analysis table.
@column seq_region_id Foreign key references to the @link seq_region table.
@column seq_region_start Sequence start position.
@column seq_region_end Sequence end position.
@column seq_region_strand Sequence region strand: 1 - forward; -1 - reverse.
@column display_label Short name for operon
@see operon_transcript
@see operon_stable_id
*/
CREATE TABLE operon (
operon_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT(2) NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
PRIMARY KEY (operon_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY name_idx (display_label)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_transcript
@desc represents polycistronic transcripts which belong to operons and encode more than one gene
@column operon_transcript_id Primary key, internal identifier.
@column analysis_id Foreign key references to the @link analysis table.
@column seq_region_id Foreign key references to the @link seq_region table.
@column seq_region_start Sequence start position.
@column seq_region_end Sequence end position.
@column seq_region_strand Sequence region strand: 1 - forward; -1 - reverse.
@column operon_id Foreign key references to the @link operon table.
@column display_label Short name for operon transcript
@see operon
@see operon_transcript_stable_id
@see operon_transcript_gene
*/
CREATE TABLE operon_transcript (
operon_transcript_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
seq_region_id INT(10) UNSIGNED NOT NULL,
seq_region_start INT(10) UNSIGNED NOT NULL,
seq_region_end INT(10) UNSIGNED NOT NULL,
seq_region_strand TINYINT(2) NOT NULL,
operon_id INT(10) UNSIGNED NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
PRIMARY KEY (operon_transcript_id),
KEY operon_idx (operon_id),
KEY seq_region_idx (seq_region_id, seq_region_start)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_transcript_gene
@desc allows association of genes with polycistronic transcripts
@column operon_transcript_id Foreign key references to the @link operon_transcript table.
@column gene_id Foreign key references to the @link gene table.
@see operon_transcript
@see gene
*/
CREATE TABLE operon_transcript_gene (
operon_transcript_id INT(10) UNSIGNED,
gene_id INT(10) UNSIGNED,
KEY operon_transcript_gene_idx (operon_transcript_id,gene_id)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_stable_id
@desc Relates operon IDs in this release to release-independent stable identifiers.
@column operon_id Primary key, internal identifier. Foreign key references to the @link operon table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see operon
*/
CREATE TABLE operon_stable_id (
operon_id INT UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (operon_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table operon_transcript_stable_id
@desc Relates operon polycistronic transcripts IDs in this release to release-independent stable identifiers.
@column operon_transcript_id Primary key, internal identifier. Foreign key references to the @link operon_transcript table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see operon_transcript
*/
CREATE TABLE operon_transcript_stable_id (
operon_transcript_id INT UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10),
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (operon_transcript_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
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