src/hg/instinct/bioInt2/bioIntDb.as 1.2

Index: src/hg/instinct/bioInt2/bioIntDb.as
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntDb.as,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/instinct/bioInt2/bioIntDb.as	20 Mar 2009 06:06:31 -0000	1.1
+++ src/hg/instinct/bioInt2/bioIntDb.as	21 Mar 2009 19:54:10 -0000	1.2
@@ -1,135 +1,166 @@
 table pathways
 "Pathway List"
 (
 uint id;            "Unique id"
 string name;        "Pathway name"
 string source;      "Pathway Source, i.e. KEGG, BioCarta"
 )
 
 table pathwayGenes
 "Pathway Genes"
 (
 uint id;            "Unique id"
 uint gene_id;	    "Gene id"
 )
 
 table pathwayInfo
 "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"
+string module;       "Analysis Module"
+string result_table; "Table containing result"
+)
+
+table analysisParams
+"All analysis parameters"
+(
+uint analysis_id;      "Module Id"
+string key;          "Parameter key"
+string val;          "Parameter val"
+)
+
 table analysisFeatures
 "All analysis features"
 (
-uint feature_id;      "Feature Id"
+uint id;              "Feature Id"
 string feature_name;  "Feature Name"
 )
 
 table analysisVals
 "All analysis vals"
 (
 uint sample_id;       "Sample Id"
-uint feature_id;      "Feature Id"
+uint feature_id;      "Analysis Feature Id"
 float val;            "Val"
 float conf;           "Confidence"
 )