The objective of this project is to extract graphs related to proteins or reactions from the data contained in the Reactome Graph database.
There are queries performed in R and Java. These are located in the respective folders for R and Java.
The program that performs the queries is a single executable ".jar" file that that creates a graph of protein interactions in a resulting ".sif" file, where the vertices are proteins and the edges are interactions between proteins. The graph represents the whole proteome available in Reactome or the interactions of a set of proteins. s
For more information check out the Wiki pages.
- Make sure java is installed as stated here.
- Download and install Neo4j
- Download and set up Reactome in Neo4j available here..
- Download the latest release of PathwayQuery. It is a .jar file. The name is PathwayQuery-X.X.jar where X.X are wild cards for the version number of the program.
- 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
- The result ".sif" file will be in the same location as the ".jar" file by default, or in the folder specified in the configuration file.