VisuNet: Accepted Rules File Format
There are two formats for rules used by VisuNet as of now: Rosetta
and Line by Line
Rosetta File Format
This format is produced by the Rosetta
program. For each rule, there are six lines.
The first line is the rule itself in the form:
IF <feature1(value1)> [AND <feature2(value2)>...] => <decision1(value1)> [ OR <decision2(value2)>...]
e.g. IF sunny(yes) AND windy(yes) => play(no)
The next lines are rule statistics in the form of:
Supp. (LHS) = [1 object(s)]
Supp. (RHS) = [1 object(s)]
Acc. (RHS) = 
Cov. (LHS) = [0.0042735]
Cov. (RHS) = [0.0357143]
Stab. (LHS) = 
Stab. (RHS) = 
Supp - Support
LHS/RHS - Left Hand Side/Right Hand Side of rule
Acc - Accuracy
Cov - Coverage
Stab - Stability
Line by Line Format
Each rule is represented in a single tab-separated line as:
<feature1(value1)>,[<feature2(value2)>...] <decision1(value1)>,[<decision2(value2)>...] <accuracy> <support>
sunny(yes),windy(yes) play(no) 3 0.75
The condition list (feature=value) and the decision list (decision=value) columns cannot have commas in the text otherwise the output may be gobbled
Color of Nodes Format
Accuracy Value Format
Use Rosetta or Line by Line file formats.
Level of the Gene Expression Format
Use the Line by Line file format.
Gene expression levels should be represented as integers:
p53(1),hsf1(2) cancer(0) 3 0.75
p53=1,hsf1=2 cancer=0 3 0.75
or string value:
p53(low),hsf1(high) cancer(0) 3 0.75
p53=low,hsf1=high cancer=0 3 0.75
Mapping File Format
The mapping file is a two-column tab-separated file containing, on each line, a condition (feature=value) and a gene short name (e.g. BRCA1) respectively.
This file is used to populate the network nodes with KEGG and GO data by matching a feature to a gene it represents and is therefore only useful if you have genomic data. This includes microarray data, CpG sites, Histone Methylations that can be mapped to specific genes.