causal-priors-extractor

This project extracts causal priors from Pathway Commons database to use in CausalPath.

Inputs

1. A BioPAX file downloaded from Pathway Commons. See https://www.pathwaycommons.org/archives/PC2/

2. A blacklist file that provides a classification for ubiquitous small molecules. This file appears in the name "blacklist.txt" in the Pathway Commons archives.

Make sure that the BioPAX file and the blacklist file come from the same directory in the archive.

Output

Causal priors as a SIF file.

How to build with Maven

git pull https://github.com/PathwayAndDataAnalysis/causal-priors-extractor.git
cd causal-priors-extractor
mvn clean install
mvn assembly:single

The last command should create cpe.jar under causal-priors-extractor/target directory. Then you can run the code by

java -jar target/cpe.jar <biopax-filename> <blacklist-filename> <output-filename>