Name: HVSM
VERSION: 1.0
This explains how to use the HVSM package. This package could calculate the gene or term similarity on yeast and human with cc, bp or mf category in Gene Ontology. If you hava any problems with how to use it, send an email to KeJia:
[email protected]
HVSM is a novel approach that measures GO term similarity by incorporating information from gene co-function networks in addition to using GO structure and their annotations.

Requirements This package requires Windows 7 with JRE 1.8 or JDK 1.8 installed.

you got three files:

data: data source used
HVSM.jar: HVSM runnable file
HVSM.ini: HVSM configuration file

java -jar HVSM.jar -org [orgonism] -db [GO category] [-gene] [-termset] -i [input] -o [output]

-db C, P or F, denotes the Database of GO, only in gene pair matching mode.
-gene Choose Gene Pair to calculate the similarity.
-h Print help information
-i The input file of termset or gene pair, split with
"tab".input termset need split with ",", eg: a,b,c
d,e,f
-o The output file of similarity, if not specified, result will output to console.
-org human or yeast, orgonism of datasets.
-termset Choose TermSet to calculate the similarity.

For example,
Calculte the similarity between termset from input
java -jar HVSM.jar -org human -termset -i data\termset_example.txt
output will be like this:
0.0
0.1831020481113516
1.2060201638430177
0.15344968111913673
0.0
0.7506287674848676
0.3337400599575926
0.1534608211421122
0.12242461565800263
0.49067429375098043
it corresponding to termsets put in the input file, one termset pair one line.

Calculte the similarity between gene pair from input file, and output to an specified file.
java -jar HVSM.jar -org human -db C -gene -i data\gene_example.txt -o output.txt
output will be like this:
0.0
0.1831020481113516
1.2060201638430177
0.15344968111913673
0.0
0.7506287674848676
0.3337400599575926
0.1534608211421122
0.12242461565800263
0.49067429375098043
0.1899425373921889
it corresponding to gene pairs put in the input file, one gene pair one line.