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 shell $ export CLASSPATH=/path/STANFORD_CORENLP/stanford-corenlp-full-2017-06-09/*
2. Create new dir in source shell $ cd source $ mkdir newdir
3. Save your text file with sentences in newdir
4. Run python script with Python 3.x shell $ cd bind $ python specie_annotation.py --file ../source/newdir/sentences.txt

Acknowledgments

This work was supported by UNAM-PAPIIT IA203420.