Carlos-Francisco Méndez-Cruz

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1 +# Organism annotation in sentences with regulatory interactions
2 +
3 +## Installation
4 +1. Download CoreNLP from https://stanfordnlp.github.io/CoreNLP/download.html
5 +2. Python modules progress and OGER:
6 +```shell
7 +$ pip3 install progress
8 +$ pip3 install git+https://github.com/OntoGene/OGER.git
9 +```
10 +## Run
11 +1. Set CLASSPATH
12 +```shell
13 +$ export CLASSPATH=/path/STANFORD_CORENLP/stanford-corenlp-full-2017-06-09/*
14 +```
15 +2. Create new dir in source
16 +```shell
17 +$ cd source
18 +$ mkdir newdir
19 +```
20 +3. Save your text file with sentences in newdir
21 +4. Run python script with Python 3.x
22 +```shell
23 +$ cd bind
24 +$ python specie_annotation.py --file ../source/newdir/sentences.txt
25 +```
26 +
27 +## Acknowledgments
28 +This work was supported by UNAM-PAPIIT IA203420.
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