clinical-lm-datasets

Setup

pip install -e .
python -m spacy download en_core_web_sm
pip install git+https://github.com/titipata/scipdf_parser
pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.3/en_core_sci_sm-0.5.3.tar.gz

Downloading guidelines

On local machine that has Chrome access:

• Install Java 17
• Install Node

Commands shown for Mayo:

export PATH_TO_SCRAPERS='{{ INSERT DESIRED OUTPUT DIRECTORY }}
export PATH_TO_RAW=$PATH_TO_SCRAPERS"/raw"  # Raw scraped guidelines directory
export PATH_TO_CLEAN=$PATH_TO_SCRAPERS"/clean" # Clean guidelines directory
cd guidelines/scrapers/mayo
npm install --silent
tsc
node js/index.js