src/hg/instinct/bioInt2/bioIntDb.sql 1.5

Index: src/hg/instinct/bioInt2/bioIntDb.sql
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntDb.sql,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/instinct/bioInt2/bioIntDb.sql	29 Mar 2009 01:40:43 -0000	1.4
+++ src/hg/instinct/bioInt2/bioIntDb.sql	27 Apr 2009 06:15:48 -0000	1.5
@@ -3,26 +3,26 @@
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
 #Pathway List
-CREATE TABLE pathways (
+CREATE TABLE genesets (
     id int unsigned not null,	# Unique id
     name varchar(255) not null,	# Pathway name
     source varchar(255) not null,	# Pathway Source, i.e. KEGG, BioCarta
               #Indices
     PRIMARY KEY(id)
 );
 
 #Pathway Genes
-CREATE TABLE pathwayGenes (
+CREATE TABLE genesetGenes (
     id int unsigned not null,	# Unique id
     gene_id int unsigned not null,	# Gene id
               #Indices
     PRIMARY KEY(id)
 );
 
 #Pathway Information
-CREATE TABLE pathwayInfo (
+CREATE TABLE genesetInfo (
     id int unsigned not null,	# Unique id
     description longblob not null,	# Description of pathway
               #Indices
     PRIMARY KEY(id)
@@ -52,10 +52,8 @@
     type_id int unsigned not null,	# Type of genomics data
     num_samples int unsigned not null,	# Number of samples in study
     name varchar(255) not null,	# Dataset name
     data_table varchar(255) not null,	# Array Data tablename
-    probe_table varchar(255) not null,	# Probe tablename
-    probe_to_gene_table varchar(255) not null,	# Probe to gene tablename
               #Indices
     PRIMARY KEY(id)
 );
 
@@ -74,35 +72,8 @@
               #Indices
     PRIMARY KEY(dataset_id)
 );
 
-#Lookup table linking knownGene
-CREATE TABLE geneLookup (
-    id int unsigned not null,	# Unique Id
-    kgId varchar(255) not null,	# Known Gene Id
-              #Indices
-    PRIMARY KEY(id)
-);
-
-#Probe Information
-CREATE TABLE probeInfo (
-    id int unsigned not null,	# Unique Id
-    chrom varchar(255) not null,	# Chromosome
-    start int unsigned not null,	# Start Base
-    stop int unsigned not null,	# Stop Base
-    name varchar(255) not null,	# Probe Name
-              #Indices
-    PRIMARY KEY(id)
-);
-
-#Lookup table linking probe id and gene id
-CREATE TABLE probeToGene (
-    probe_id int unsigned not null,	# Probe Id
-    gene_id int unsigned not null,	# Gene Id
-              #Indices
-    PRIMARY KEY(probe_id)
-);
-
 #Probe values for single sample
 CREATE TABLE probeSampleVal (
     probe_id int unsigned not null,	# Probe Id
     sample_id int unsigned not null,	# Sample Id
@@ -126,9 +97,8 @@
     name varchar(255) not null,	# Sample Name
     patient_id int unsigned not null,	# Patient Id
     patient_name varchar(255) not null,	# Patient Name
     dataset_id int unsigned not null,	# Dataset Id
-    exp_id int unsigned not null,	# Index in dataset -- for probeVals format
     tissue_id int unsigned not null,	# Tissue Type Id
               #Indices
     PRIMARY KEY(id)
 );
@@ -185,8 +155,9 @@
 #All analysis features
 CREATE TABLE analysisFeatures (
     id int unsigned not null,	# Feature Id
     feature_name varchar(255) not null,	# Feature Name
+    type varchar(255) not null,	# Feature Type
               #Indices
     PRIMARY KEY(id)
 );