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Carlos-Francisco Méndez-Cruz
/
bacteria-annotation
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Authored by
Carlos-Francisco Méndez-Cruz
2022-03-22 02:55:05 -0600
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# 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:
```
shell
$
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.
\ No newline at end of file
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