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 1000000 -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
@@ -1,190 +1,164 @@
-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"
 )
 
 table tissues
 "All available issues"
 (
 uint id;            "Unique id"
 string name;        "Tissue Type"
 )
 
 table dataTypes
 "All available data types"
 (
 uint id;            "Unique id"
 string format;      "Data Format"
 string name;        "Data type"
 )
 
 table datasets
 "All available datasets"
 (
 uint id;            "Unique Id"
 uint tissue_id;     "Numeric id denoting tissue type"
 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"
 (
 uint id;             "Cohort Id"
 string name;         "Cohort name"
 )
 
 table datasetCohort
 "Dataset cohort lookup"
 (
 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"
 uint sample_id;     "Sample Id"
 float val;          "Exp Value"
 )
 
 table probeVals
 "Probe values for all samples"
 (
 uint probe_id;      "Probe Id"
 uint sample_count;  "Sample Count"
 float[sample_count] sample_data; "Sample Data"
 )
 
 table samples
 "All sample info"
 (
 uint id;             "Unique Id"
 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
 "All Features"
 (
 uint id;             "Unique Id"
 string name;         "Feature Name"
 string shortLabel;   "Short Label"
 string longLabel;    "Long Label"
 )
 
 table clinicalData
 "All clinical data"
 (
 uint sample_id;      "Sample Id"
 uint feature_id;     "Feature Id"
 double val;          "Value"
 string code;         "Coded Value"
 )
 
 table analyses
 "All analyses run"
 (
 uint id;             "Analysis id"
 uint cohort_id;      "Cohort Id"
 uint module_id;      "Module Id"
 string result_table; "Table containing result"
 lstring input_tables; "Comma-separated list of input tables"
 )
 
 table analysisModules
 "All analysis modules"
 (
 uint id;             "Module Id"
 string name;         "Module Name"
 string type;         "Module Type (gene, geneset, etc.)"
 )
 
 table analysisParams
 "All analysis parameters"
 (
 uint analysis_id;      "Analysis Id"
 string name;           "Parameter name"
 string val;            "Parameter val"
 )
 
 table analysisFeatures
 "All analysis features"
 (
 uint id;              "Feature Id"
 string feature_name;  "Feature Name"
+string type;          "Feature Type"
 )
 
 table analysisVals
 "All analysis vals"
 (
 uint sample_id;       "Sample Id"
 uint feature_id;      "Analysis Feature Id"
 float val;            "Val"
 float conf;           "Confidence"
 )
 
 table cohortCorr
 "Cohort Correlation tables"
 (
 uint cohort_id;       "Cohort Id"
 string result_table;  "Result Table"
 )
 
 table corrResults
 "Correlation results"
 (
 uint feature_id1;     "Feature Id1"
 uint feature_id2;     "Feature Id2"
 float val;            "Correlation Value"
 )

