Installation

Getting started with BioMedICUS

Prerequisites

• Python 3.5+
• Java JDK 9.0+. Note, you will need to have the “java” command on the your “$PATH”.

Virtual Environment

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

Windows

pip3 install virtualenv
python3 -m virtualenv biomedicus_venv
biomedicus_venv\Scripts\activate

PyTorch

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.

Installation

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.