From 65d14b7f15d56340f05ee0999e4d17962d90e918 Mon Sep 17 00:00:00 2001
From: Dan Staines <dstaines@ebi.ac.uk>
Date: Mon, 15 Aug 2011 12:44:04 +0000
Subject: [PATCH] added docs for operon-related tables

---
 sql/table.sql | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)

diff --git a/sql/table.sql b/sql/table.sql
index 309f9b9515..6e72b4ebcc 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -2470,6 +2470,21 @@ 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,
@@ -2484,6 +2499,23 @@ CREATE TABLE operon (
   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,
@@ -2499,6 +2531,16 @@ CREATE TABLE operon_transcript (
   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,
@@ -2506,6 +2548,19 @@ CREATE TABLE operon_transcript_gene (
   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,
@@ -2517,6 +2572,19 @@ CREATE TABLE operon_stable_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,
-- 
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