- 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
- Stanza is a python wrapper for Stanford CoreNLP and PyTorch NLP models.
- tregex for chunking
- neural pipelien for dependency parsing
- Given a sentence and a list of triggers,
- Check if a trigger is fired.
- If a trigger is fired, run a dependency parser and a chunker on the sentence.
- Using the dependency relations of the trigger, identify head words.
- Extract noun phrases by merging dependency relations and chunks based on the head words.
-
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
- Biomedical Named Entity Recognisers can be used to improve NP chunking and to identify the roles on NPs.