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Commit 7627278d authored by Magali Ruffier's avatar Magali Ruffier
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data_file moved to features and analyses section, interpro moved to external references section 

miscellaneous section removed
removed hard coded html tags for schema file, this is now at the top of the file
merged two description tags for interpro table, was only using the second one
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sql/table.sql
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......@@ -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;
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