From b47341cc09f8ff9e47d784274e36b5c31a6200b9 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 23 Jul 2012 10:42:52 +0000
Subject: [PATCH] schema for xref mindmap db
---
.../xref_mapping/xref_mindmap/sql/tables.sql | 72 +++++++++++++++++++
1 file changed, 72 insertions(+)
create mode 100644 misc-scripts/xref_mapping/xref_mindmap/sql/tables.sql
diff --git a/misc-scripts/xref_mapping/xref_mindmap/sql/tables.sql b/misc-scripts/xref_mapping/xref_mindmap/sql/tables.sql
new file mode 100644
index 0000000000..58f5bfae22
--- /dev/null
+++ b/misc-scripts/xref_mapping/xref_mindmap/sql/tables.sql
@@ -0,0 +1,72 @@
+CREATE TABLE external_db_type (
+ external_db_id INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+ db_name VARCHAR(100) NOT NULL,
+ db_display_name VARCHAR(255),
+ db_type_id INTEGER UNSIGNED,
+
+ PRIMARY KEY (external_db_id),
+ KEY type_idx (db_type_id, db_name)
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+
+CREATE TABLE object_xref_linkage (
+ external_db_id INTEGER UNSIGNED NOT NULL,
+ ensembl_object_type VARCHAR(100),
+ link_type_id INTEGER UNSIGNED NOT NULL,
+ linked_external_db_id INTEGER UNSIGNED,
+ linked_node_text VARCHAR(255),
+
+ KEY xref_origin_idx (external_db_id, ensembl_object_type)
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+CREATE TABLE object_external_db_node (
+ ensembl_object_type VARCHAR(100) NOT NULL,
+ external_db_id INTEGER UNSIGNED NOT NULL,
+ mindmap_tag_id VARCHAR(100) NOT NULL,
+
+ UNIQUE KEY (ensembl_object_type, external_db_id)
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+
+CREATE TABLE db_type (
+ db_type_id INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+ db_type VARCHAR(255) NOT NULL,
+
+ PRIMARY KEY (db_type_id)
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+CREATE TABLE link_type (
+ link_type_id INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+ link_type VARCHAR(100) NOT NULL,
+ link_description VARCHAR(255) NOT NULL,
+
+ PRIMARY KEY (link_type_id),
+ KEY link_type_idx (link_type)
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+CREATE TABLE object_distance (
+ from_object VARCHAR(100) NOT NULL,
+ to_object VARCHAR(100) NOT NULL,
+ distance TINYINT(1) UNSIGNED NOT NULL,
+
+ KEY (from_object,distance)
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+LOCK TABLES `object_distance` WRITE;
+INSERT INTO `object_distance` VALUES ('Gene','Gene',0), ('Gene','Transcript',1), ('Gene', 'Translation', 2), ('Transcript','Gene',1), ('Transcript','Transcript',0), ('Transcript', 'Translation', 1), ('Translation', 'Gene', 2), ('Translation', 'Transcript',1), ('Translation', 'Translation',0);
+UNLOCK TABLES;
+
+LOCK TABLES `db_type` WRITE;
+INSERT INTO `db_type` VALUES (1,'disease related'),(2,'expression'),(3,'integrated information'),(4,'naming'),(5,'products'),(6,'sequence/annotation'),(7,'classification'),(8,'function/location'),(9,'structure'),(10,'other resources');
+UNLOCK TABLES;
+
+LOCK TABLES `link_type` WRITE;
+INSERT INTO `link_type` VALUES (1,'DIRECT', 'DIRECT'),(2,'INFERRED PAIR', 'INFERRED_PAIR'),(3,'DEPENDENT', 'DEPENDENT ON'),(4,'SEQUENCE_MATCH', 'SEQUENCE MATCH'),(5,'COORDINATE_OVERLAP', 'COORDINATE OVERLAP'),(6,'GENERATED_FROM', 'GENERATED FROM'),(7,'PROJECTION','PROJECTION'),(8,'PROTEIN_FEATURES', 'VIA PROTEIN FEATURES');
+UNLOCK TABLES;
+
+
+
--
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