Index: src/hg/instinct/bioInt2/bioIntDb.as
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntDb.as,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/instinct/bioInt2/bioIntDb.as	29 Mar 2009 01:40:42 -0000	1.4
+++ src/hg/instinct/bioInt2/bioIntDb.as	27 Apr 2009 06:15:48 -0000	1.5
@@ -1,20 +1,20 @@
-table pathways
+table genesets
 "Pathway List"
 (
 uint id;            "Unique id"
 string name;        "Pathway name"
 string source;      "Pathway Source, i.e. KEGG, BioCarta"
 )
 
-table pathwayGenes
+table genesetGenes
 "Pathway Genes"
 (
 uint id;            "Unique id"
 uint gene_id;	    "Gene id"
 )
 
-table pathwayInfo
+table genesetInfo
 "Pathway Information"
 (
 uint id;             "Unique id"
 lstring description; "Description of pathway"
@@ -43,10 +43,8 @@
 uint type_id;       "Type of genomics data"
 uint num_samples;   "Number of samples in study"
 string name;        "Dataset name"
 string data_table;  "Array Data tablename"  
-string probe_table; "Probe tablename"
-string probe_to_gene_table; "Probe to gene tablename"
 )
 
 table cohorts
 "All cohorts"
@@ -61,32 +59,8 @@
 uint dataset_id;     "Dataset Id"
 uint cohort_id;      "Cohort Id"
 )
 
-table geneLookup
-"Lookup table linking knownGene"
-(
-uint id;            "Unique Id"
-string kgId;        "Known Gene Id"
-)
-
-table probeInfo
-"Probe Information"
-(
-uint id;            "Unique Id"
-string chrom;       "Chromosome"
-uint start;         "Start Base"
-uint stop;          "Stop Base"
-string name;        "Probe Name"
-)
-
-table probeToGene
-"Lookup table linking probe id and gene id"
-(
-uint probe_id;      "Probe Id"
-uint gene_id;       "Gene Id"
-)
-
 table probeSampleVal
 "Probe values for single sample"
 (
 uint probe_id;      "Probe Id"
@@ -109,9 +83,8 @@
 string name;         "Sample Name"
 uint patient_id;     "Patient Id"
 string patient_name; "Patient Name"
 uint dataset_id;     "Dataset Id"
-uint exp_id;         "Index in dataset -- for probeVals format"
 uint tissue_id;      "Tissue Type Id"
 )
 
 table features
@@ -162,8 +135,9 @@
 "All analysis features"
 (
 uint id;              "Feature Id"
 string feature_name;  "Feature Name"
+string type;          "Feature Type"
 )
 
 table analysisVals
 "All analysis vals"

