SPO extractor using Stanza

Example sentences and universal dependencies

• The encapsulation of rifampicin leads to a reduction of the Mycobacterium smegmatis inside macrophages.
• nsubj (nominal subject) <= VERB => obl (oblique nominal)

• The Norwalk virus is the prototype virus that causes epidemic gastroenteritis infecting predominantly older children and adults.
• acl:relcl (adjectival clause) => VERB => obj (object)

• It is widely agreed that the exposure to ambient air pollution may cause serious respiratory illnesses and that weather conditions may also contribute to the seriousness.
• nsubj <= VERB => obj

• In this report, ribavirin was shown to inhibit SARS coronavirus replication in five different cell types of animal or human origin at therapeutically achievable concentrations.
• nsubj:pass <= xcomp => VERB => obj

• Chronic hepatitis virus infection is a major cause of chronic hepatitis, cirrhosis, and hepatocellular carcinoma worldwide.
• nsubj <= NOUN => nmod => conj
• coordinating conjunctions

What is Stanza?

• Stanza is a python wrapper for Stanford CoreNLP and PyTorch NLP models.
• tregex for chunking
• neural pipelien for dependency parsing

Algorithm

1. Given a sentence and a list of triggers,
2. Check if a trigger is fired.
3. If a trigger is fired, run a dependency parser and a chunker on the sentence.
4. Using the dependency relations of the trigger, identify head words.
5. Extract noun phrases by merging dependency relations and chunks based on the head words.

Usages

• Download Stanford CoreNLP and an English models

• Put the model jars in the distribution folder

• Setting up environment variables

export CORENLP_HOME=/path/to/stanford-corenlp-full-2020-04-20
export DATA_DIR=/path/to/data/

• How to install dependencies?

pip install -r requirements.txt

• Download a model for a neural dependency parser

python -c 'import stanza; stanza.download("en")'

• How to run tests?

cd /path/to/project-directory
pytest tests/test_SPOs.py

export DATA_DIR="$(pwd)/data/tests"
pytest tests/test_data_reader.py

• How to get SPOs for example sentences

PYTHONPATH=. python tests/test_SPOs.py

• How to extract SPO?

PYTHONPATH=. python bin/run_spo.py -i input_directory -o output_file

What is missing?

• Biomedical Named Entity Recognisers can be used to improve NP chunking and to identify the roles on NPs.