Java How to run

• Open a command prompt located in the folder that contains the "PathwayQuery-X.X.jar" file.
• (optionally) Create a file called "config.txt" in the same folder, and set the desired values for the configuration parameters.
• Execute the following instruction in the command prompt:

java -jar PathwayQuery-X.X.jar [options]

• The result ".sif" file will be in the same location as the ".jar" file by default, or in the folder specified by the configuration file.

Examples

Extract graph where all proteins are participants of reactions that have a publication reference before/at some year.

Extract graph where the input set of proteins are participants of reactions with a reference publication before some year.

Example Input:

Command:

Example Output:

Extract graph where the input set of proteins are participants of reactions with a reference publication from a specific year.