Metadata-Version: 2.1
Name: biomedicus
Version: 3.0b1
Summary: A biomedical and clinical NLP engine.
Home-page: https://nlpie.github.io/biomedicus
Author: University of Minnesota NLP/IE Group
Author-email: nlp-ie@umn.edu
License: UNKNOWN
Keywords: nlp biomedical text
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Information Technology
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Java
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Text Processing :: General
Classifier: Topic :: Text Processing :: Linguistic
Requires-Python: ~=3.5
Description-Content-Type: text/markdown
Requires-Dist: mtap
Requires-Dist: numpy
Requires-Dist: pyyaml
Requires-Dist: regex
Requires-Dist: tqdm
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Provides-Extra: tests
Requires-Dist: pytest-runner ; extra == 'tests'
Requires-Dist: pytest ; extra == 'tests'
Provides-Extra: torch
Requires-Dist: torch ; extra == 'torch'
Provides-Extra: torch-gpu
Requires-Dist: torch-gpu ; extra == 'torch-gpu'

# BioMedICUS

The BioMedical Information Collection and Understanding System (BioMedICUS) is a system for large-scale text analysis and processing of biomedical and clinical reports. The system is being developed by the Natural Language Processing and Information Extraction Program at the University of Minnesota Institute for Health Informatics.

This is a collaborative project that aims to serve biomedical and clinical researchers, allowing for customization with different texts.

More information about BioMedICUS can be found on our [website](https://nlpie.github.io/biomedicus). 

## Prerequisites

- [Python 3.5 or later](https://www.python.org/)
- [Java JDK 8.0 or later](https://adoptopenjdk.net/index.html). Note, you will need to have the ["java" command on the your "$PATH"](https://www.java.com/en/download/help/path.xml).

## Installation

```bash
pip install biomedicus\[torch]
```

## Deploying the default BioMedICUS Pipeline

The following command runs a script that will start up all of the BioMedICUS services for processing clinical notes:

```bash
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:

```bash
biomedicus run /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.

## Contact

BioMedICUS is developed by the [NLP/IE Group](https://healthinformatics.umn.edu/research/nlpie-group) at the University of Minnesota Institute for Health Informatics. You can contact us at [nlp-ie@umn.edu](mailto:nlp-ie@umn.edu).

