diff --git a/sql/table.sql b/sql/table.sql
index 190d3d89363497cf8d79e959338ec8f4957115a5..a61584eba5ee08cbb9707e9a27253622af67e152 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -9,9 +9,7 @@
/**
@header Fundamental Tables
-@desc A PDF document of the schema is available <a href="fundamental_tables_core.pdf" target="_blank">here</a>.<br />
-<a href="fundamental_tables_core.pdf" target="_blank">
-<img border="0" src="fundamental_tables_thumb.png" alt="Fundamental Tables Schema Diagram" style="margin-left:20px; margin-top:20px;" /></a>
+@colour #000
*/
@@ -323,6 +321,7 @@ PRIMARY KEY (intron_supporting_evidence_id, transcript_id)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
/**
@table exon_transcript
@desc Relationship table linking exons with transcripts. The rank column indicates the 5' to 3' position of the exon within the transcript, i.e. a rank of 1 means the exon is the 5' most within this transcript.
@@ -670,6 +669,32 @@ CREATE TABLE seq_region (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+/**
+@table seq_region_synonym
+@desc Allows for storing multiple names for sequence regions.
+
+@column seq_region_synonym_id Primary key, internal identifier.
+@column seq_region_id Foreign key references to the @link seq_region table.
+@column synonym Alternative name for sequence region.
+@column external_db_id Foreign key references to the @link external_db table.
+
+*/
+
+CREATE TABLE seq_region_synonym (
+
+ seq_region_synonym_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
+ seq_region_id INT(10) UNSIGNED NOT NULL,
+ synonym VARCHAR(40) NOT NULL,
+ external_db_id INTEGER UNSIGNED,
+
+ PRIMARY KEY (seq_region_synonym_id),
+ UNIQUE KEY syn_idx (synonym),
+ KEY seq_region_idx (seq_region_id)
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+
+
/**
@table seq_region_attrib
@@ -873,9 +898,6 @@ CREATE TABLE unconventional_transcript_association (
/**
@header Features and Analyses
-@desc A PDF document of the schema is available <a href="features_analyses_core.pdf" target="_blank">here</a>.<br />
-<a href="features_analyses_core.pdf" target="_blank">
-<img border="0" src="features_analyses_thumb.png" alt="Features and Analyses Schema Diagram" style="margin-left:20px; margin-top:20px;" /></a>
*/
@@ -1979,12 +2001,41 @@ CREATE TABLE transcript_supporting_feature (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+/**
+@table data_file
+@desc Allows the storage of flat file locations used to store large quanitities of data currently unsuitable in a traditional database table.
+
+@column data_file_id Auto-increment surrogate primary key
+@column coord_system_id Coordinate system this file is linked to. Used to decipher the assembly version it was mapped to
+@column analysis_id Analysis this file is linked to
+@column name Name of the file
+@column version_lock Indicates that this file is only compatible with the current Ensembl release version
+@column absolute Flags that the URL given is fully resolved and should be used without question
+@column url Optional path to the file (can be absolute or relative)
+@column file_type Type of file e.g. BAM, BIGBED, BIGWIG and VCF
+*/
+
+CREATE TABLE data_file (
+ data_file_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ coord_system_id INT(10) UNSIGNED NOT NULL,
+ analysis_id SMALLINT UNSIGNED NOT NULL,
+ name VARCHAR(100) NOT NULL,
+ version_lock TINYINT(1) DEFAULT 0 NOT NULL,
+ absolute TINYINT(1) DEFAULT 0 NOT NULL,
+ url TEXT,
+ file_type ENUM('BAM','BIGBED','BIGWIG','VCF'),
+
+ PRIMARY KEY (data_file_id),
+ UNIQUE KEY df_unq_idx(coord_system_id, analysis_id, name, file_type),
+ INDEX df_name_idx(name),
+ INDEX df_analysis_idx(analysis_id)
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+
+
/**
@header ID Mapping
-@desc A PDF document of the schema is available <a href="id_mapping_core.pdf" target="_blank">here</a>.<br />
-<a href="id_mapping_core.pdf" target="_blank">
-<img border="0" src="id_mapping_thumb.png" alt="ID Mapping Schema Diagram" style="margin-left:20px; margin-top:20px;" /></a>
*/
/**
@@ -2169,9 +2220,6 @@ CREATE TABLE seq_region_mapping (
/**
@header External References
-@desc A PDF document of the schema is available <a href="xrefs_core.pdf" target="_blank">here</a>.<br />
-<a href="xrefs_core.pdf" target="_blank">
-<img border="0" src="xrefs_thumb.png" alt="External References Schema Diagram" style="margin-left:20px; margin-top:20px;" /></a>
*/
@@ -2451,32 +2499,6 @@ CREATE TABLE associated_group (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-/**
-@table seq_region_synonym
-@desc Allows for storing multiple names for sequence regions.
-
-@column seq_region_synonym_id Primary key, internal identifier.
-@column seq_region_id Foreign key references to the @link seq_region table.
-@column synonym Alternative name for sequence region.
-@column external_db_id Foreign key references to the @link external_db table.
-
-*/
-
-CREATE TABLE seq_region_synonym (
-
- seq_region_synonym_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
- seq_region_id INT(10) UNSIGNED NOT NULL,
- synonym VARCHAR(40) NOT NULL,
- external_db_id INTEGER UNSIGNED,
-
- PRIMARY KEY (seq_region_synonym_id),
- UNIQUE KEY syn_idx (synonym),
- KEY seq_region_idx (seq_region_id)
-
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-
-
/**
@table unmapped_object
@@ -2587,22 +2609,14 @@ CREATE TABLE xref (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-
-/**
-@header Miscellaneous
-@desc Other tables
-*/
-
-
/**
@table interpro
@desc Allows storage of links to the InterPro database. InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
+ <a href="http://www.ebi.ac.uk/interpro/">InterPro</a> - The InterPro website
@column interpro_ac InterPro protein accession number.
@column id InterPro protein id.
-@desc <a href="http://www.ebi.ac.uk/interpro/">InterPro</a> - The InterPro website
-
*/
@@ -2615,33 +2629,3 @@ CREATE TABLE interpro (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-/**
-@table data_file
-@desc Allows the storage of flat file locations used to store large quanitities of data currently unsuitable in a traditional database table.
-
-@column data_file_id Auto-increment surrogate primary key
-@column coord_system_id Coordinate system this file is linked to. Used to decipher the assembly version it was mapped to
-@column analysis_id Analysis this file is linked to
-@column name Name of the file
-@column version_lock Indicates that this file is only compatible with the current Ensembl release version
-@column absolute Flags that the URL given is fully resolved and should be used without question
-@column url Optional path to the file (can be absolute or relative)
-@column file_type Type of file e.g. BAM, BIGBED, BIGWIG and VCF
-*/
-
-CREATE TABLE data_file (
- data_file_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
- coord_system_id INT(10) UNSIGNED NOT NULL,
- analysis_id SMALLINT UNSIGNED NOT NULL,
- name VARCHAR(100) NOT NULL,
- version_lock TINYINT(1) DEFAULT 0 NOT NULL,
- absolute TINYINT(1) DEFAULT 0 NOT NULL,
- url TEXT,
- file_type ENUM('BAM','BIGBED','BIGWIG','VCF'),
-
- PRIMARY KEY (data_file_id),
- UNIQUE KEY df_unq_idx(coord_system_id, analysis_id, name, file_type),
- INDEX df_name_idx(name),
- INDEX df_analysis_idx(analysis_id)
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
-