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Commit 6b2fb651 authored by Monika Komorowska's avatar Monika Komorowska
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merge stable_id tables with object tables

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sql/table.sql
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......@@ -224,6 +224,10 @@ Note seq_region_start is always less that seq_region_end, i.e. when the exon is
@column end_phase Usually, end_phase = (phase + exon_length)%3 but end_phase could be -1 if the exon is half-coding and its 3 prime end is UTR.
@column is_current
@column is_constitutive
@column stable_id Release-independent stable identifier.
@column version Stable identifier version number.
@column created_date Date created.
@column modified_date Date modified.
@see exon_transcript
......@@ -243,36 +247,13 @@ CREATE TABLE exon (
is_current BOOLEAN NOT NULL DEFAULT 1,
is_constitutive BOOLEAN NOT NULL DEFAULT 0,
PRIMARY KEY (exon_id),
KEY seq_region_idx (seq_region_id, seq_region_start)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table exon_stable_id
@desc Relates exon IDs in this release to release-independent stable identifiers.
@column exon_id Primary key, internal identifier.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see stable_id
*/
CREATE TABLE exon_stable_id (
exon_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10) NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (exon_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
......@@ -325,6 +306,10 @@ CREATE TABLE exon_transcript (
@column is_current
@column canonical_transcript_id Foreign key references to the @link transcript table.
@column canonical_annotation Canonical annotation.
@column stable_id Release-independent stable identifier.
@column version Stable identifier version number.
@column created_date Date created.
@column modified_date Date modified.
@see transcript
......@@ -347,11 +332,16 @@ CREATE TABLE gene (
is_current BOOLEAN NOT NULL DEFAULT 1,
canonical_transcript_id INT(10) UNSIGNED NOT NULL,
canonical_annotation VARCHAR(255) DEFAULT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (gene_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY xref_id_index (display_xref_id),
KEY analysis_idx (analysis_id)
KEY analysis_idx (analysis_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
......@@ -382,35 +372,6 @@ CREATE TABLE gene_attrib (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table gene_stable_id
@desc Relates gene IDs in this release to release-independent stable identifiers.
@column gene_id Primary key, internal identifier. Foreign key references to the @link gene table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see gene
@see stable_id
*/
CREATE TABLE gene_stable_id (
gene_id INT UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10) NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (gene_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table karyotype
@desc Describes bands that can be stained on the chromosome.
......@@ -479,17 +440,14 @@ CREATE TABLE IF NOT EXISTS meta (
# Add schema type and schema version to the meta table.
INSERT INTO meta (species_id, meta_key, meta_value) VALUES
(NULL, 'schema_type', 'core'),
(NULL, 'schema_version', '64');
(NULL, 'schema_version', '65');
# Patches included in this schema file:
# NOTE: At start of release cycle, remove patch entries from last release.
# NOTE: Avoid line-breaks in values.
INSERT INTO meta (species_id, meta_key, meta_value) VALUES
(NULL, 'patch', 'patch_63_64_a.sql|schema_version'),
(NULL, 'patch', 'patch_63_64_b.sql|add_operons'),
(NULL, 'patch', 'patch_63_64_c.sql|is_ref_added_to_alt_allele'),
(NULL, 'patch', 'patch_63_64_d.sql|linkage_type change in ontology_xref');
(NULL, 'patch', 'patch_64_65_a.sql|schema_version'),
(NULL, 'patch', 'patch_64_65_b.sql|merge_stable_id_with_object');
/**
@table meta_coord
......@@ -526,6 +484,10 @@ CREATE TABLE meta_coord (
@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
@column stable_id Release-independent stable identifier.
@column version Stable identifier version number.
@column created_date Date created.
@column modified_date Date modified.
@see operon_transcript
@see operon_stable_id
......@@ -538,38 +500,18 @@ CREATE TABLE operon (
seq_region_strand TINYINT(2) NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
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 name_idx (display_label),
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
......@@ -582,6 +524,10 @@ CREATE TABLE operon_stable_id (
@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
@column stable_id Release-independent stable identifier.
@column version Stable identifier version number.
@column created_date Date created.
@column modified_date Date modified.
@see operon
@see operon_transcript_stable_id
......@@ -596,34 +542,14 @@ CREATE TABLE operon_transcript (
operon_id INT(10) UNSIGNED NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
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 seq_region_idx (seq_region_id, seq_region_start),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
......@@ -726,7 +652,10 @@ Note that a transcript is usually associated with a translation, but may not be,
@column description Transcript description.
@column is_current
@column canonical_translation_id Foreign key references to the @link canonical_translation table.
@column stable_id Release-independent stable identifier.
@column version Stable identifier version number.
@column created_date Date created.
@column modified_date Date modified.
*/
......@@ -746,13 +675,18 @@ CREATE TABLE transcript (
description TEXT,
is_current BOOLEAN NOT NULL DEFAULT 1,
canonical_translation_id INT(10) UNSIGNED,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (transcript_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY gene_index (gene_id),
KEY xref_id_index (display_xref_id),
KEY analysis_idx (analysis_id),
UNIQUE INDEX canonical_translation_idx (canonical_translation_id)
UNIQUE INDEX canonical_translation_idx (canonical_translation_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
......@@ -784,37 +718,6 @@ CREATE TABLE transcript_attrib (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table transcript_stable_id
@desc Relates transcript IDs in this release to release-independent stable identifiers.
@column transcript_id Primary key, internal identifier. Foreign key references to the @link transcript table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see transcript
@see stable_id
*/
CREATE TABLE transcript_stable_id (
transcript_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10) NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (transcript_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table translation
@desc Describes which parts of which exons are used in translation. The seq_start and seq_end columns are 1-based offsets into the relative coordinate system of start_exon_id and end_exon_id. i.e, if the translation starts at the first base of the exon, seq_start would be 1. Transcripts are related to translations by the transcript_id key in this table.
......@@ -825,7 +728,10 @@ CREATE TABLE transcript_stable_id (
@column start_exon_id Foreign key references to the @link exon table.
@column seq_end 1-based offset into the relative coordinate system of end_exon_id.
@column end_exon_id Foreign key references to the @link exon table.
@column stable_id Release-independent stable identifier.
@column version Stable identifier version number.
@column created_date Date created.
@column modified_date Date modified.
*/
......@@ -837,9 +743,14 @@ CREATE TABLE translation (
start_exon_id INT(10) UNSIGNED NOT NULL,
seq_end INT(10) NOT NULL, # relative to exon start
end_exon_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (translation_id),
KEY transcript_idx (transcript_id)
KEY transcript_idx (transcript_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
......@@ -871,36 +782,6 @@ CREATE TABLE translation_attrib (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table translation_stable_id
@desc Relates translation IDs in this release to release-independent stable identifiers.
@column translation_id Primary key, internal identifier. Foreign key references to the @link translation table.
@column stable_id Stable identifier.
@column version Version number.
@column created_date Date created.
@column modified_date Date modified.
@see translation
@see stable_id
*/
CREATE TABLE translation_stable_id (
translation_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) NOT NULL,
version INT(10) NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL,
modified_date DATETIME NOT NULL,
PRIMARY KEY (translation_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table unconventional_transcript_association
@desc Describes transcripts that do not link to a single gene in the normal way.
......@@ -2603,3 +2484,16 @@ CREATE TABLE interpro (
KEY id_idx (id)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
CREATE VIEW exon_stable_id (exon_id, stable_id, version, created_date, modified_date) AS (SELECT exon_id, stable_id, version, created_date, modified_date FROM exon);
CREATE VIEW gene_stable_id (gene_id, stable_id, version, created_date, modified_date) AS (SELECT gene_id, stable_id, version, created_date, modified_date FROM gene);
CREATE VIEW operon_stable_id (operon_id, stable_id, version, created_date, modified_date) AS (SELECT operon_id, stable_id, version, created_date, modified_date FROM operon);
CREATE VIEW operon_transcript_stable_id (operon_transcript_id, stable_id, version, created_date, modified_date) AS (SELECT operon_transcript_id, stable_id, version, created_date, modified_date FROM operon_transcript);
CREATE VIEW translation_stable_id (translation_id, stable_id, version, created_date, modified_date) AS (SELECT translation_id, stable_id, version, created_date, modified_date FROM translation);
CREATE VIEW transcript_stable_id (transcript_id, stable_id, version, created_date, modified_date) AS (SELECT transcript_id, stable_id, version, created_date, modified_date FROM transcript);
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