Organism annotation in sentences with regulatory interactions

Installation

1. Download CoreNLP from https://stanfordnlp.github.io/CoreNLP/download.html
2. Python modules progress and OGER:

$ pip3 install progress
$ pip3 install git+https://github.com/OntoGene/OGER.git

Run

1. Set CLASSPATH

$ export CLASSPATH=/path/STANFORD_CORENLP/stanford-corenlp-full-2017-06-09/*

1. Create new dir in source:

$ cd source
$ mkdir newdir 

1. Save your text file with sentences in newdir
2. Run python script with Python 3.x:

$ cd bind 
$ python specie_annotation.py --file ../source/newdir/sentences.txt

Contact

Please send mail to cmendezc@ccg.unam.mx

Acknowledgments

This work was supported by UNAM-PAPIIT IA203420.