Getting started with BioMedICUS
We recommend that you use a Python 3 virtual environment, a local environment of installed packages, to avoid any dependency conflicts.
Linux / MacOS
pip3 install virtualenv python3 -m virtualenv biomedicus_venv source biomedicus_venv/bin/activate
pip3 install virtualenv python3 -m virtualenv biomedicus_venv biomedicus_venv\Scripts\activate
BioMedICUS requires PyTorch, a machine learning framework. Installation instructions for PyTorch can be found here. Select your platform and “Pip”, and “None” for CUDA unless you have a NVIDIA graphics card and have installed the CUDA toolkit.
pip3 install biomedicus
Deploying the default BioMedICUS Pipeline
The following command runs a script that will start up all of the BioMedICUS services for processing clinical notes:
biomedicus deploy --download-data
Processing a directory of text files using BioMedICUS
After deploying BioMedICUS, you can process a directory of documents using the following command:
biomedicus run --include-label-text /path/to/input_dir /path/to/output_dir
This will process the documents in the directory using BioMedICUS and save the results as json-serialized MTAP Events to output directory.