src/hg/instinct/bioInt2/bioIntDb.as 1.1

Index: src/hg/instinct/bioInt2/bioIntDb.as
===================================================================
RCS file: src/hg/instinct/bioInt2/bioIntDb.as
diff -N src/hg/instinct/bioInt2/bioIntDb.as
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/instinct/bioInt2/bioIntDb.as	20 Mar 2009 06:06:31 -0000	1.1
@@ -0,0 +1,135 @@
+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 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 analysisFeatures
+"All analysis features"
+(
+uint feature_id;      "Feature Id"
+string feature_name;  "Feature Name"
+)
+
+table analysisVals
+"All analysis vals"
+(
+uint sample_id;       "Sample Id"
+uint feature_id;      "Feature Id"
+float val;            "Val"
+float conf;           "Confidence"
+)