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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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