Variant extraction from papers

Install

• Create a virtual environment with Python-3.9 (only once):

  python3 -m venv venv

• Activate the virtual environment each time:

  source venv/bin/activate

• Install dependencies (only once):

  pip install -r requirements.txt

Train model (only once)

• Download nltk and related tools, prepare data for training and train model:

  bash train_model.sh

Configure credentials

Edit:

utils/all_config.cfg

With wbtools access credentials

Tests

• To test regexes:

python test_regexes.py

• To fetch some papers locally:

python fetch_papers.py

• To test the variant extraction on some papers

  python hybrid_extraction.py

Execution

python main.py