PathMEN Files

Introduction:

PathMen is a tool for mining biological pathway mentions from biomedical literature.  It's implemented under the GATE framework, including two major components: rule-based detection and dictionary matching. 

The rules are implemented using JAPE and the dictionary matching is a soft one. 

You can use the code in your own pipeline or you can run the executable jar file 'PathMen.jar' directly through commandline. 

A paper related to PathMen has been submitted is now under review. Currently, some data files related to the paper have not been uploaded yet. They will be available as soon as the paper is accepted. But if you need PathMen directly, please contact me via chengkun.wu@postgrad.manchester.ac.uk.

Suggestions and comments are welcome. 

=====Usage: ============================================
You can run the PathMen jar file directly to have a test.

Examples:

1. See the results on a test str (preset): java -jar PathMen.jar
2. See the results on gold corpus: java -jar PathMen.jar --test gold
3. See the results on a test file: java -jar PathMen.jar --test test
4. See the results on your file: java -jar PathMen.jar --test YOUR_FILE

If you want to process a large file, you might need to add Java Virtual Machine parameters. For instance, 

java -Xmx4G -jar PathMen.jar --test YOUR_FILE