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Code for the old version of BioMedICUS, for the new version see the biomedicus3 repository.

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# New Version

BioMedICUS has a new version: https://github.com/nlpie/biomedicus

The code on this repository is mature but will not be receiving any further updates.

[![](https://zenodo.org/badge/51161341.svg)](https://zenodo.org/badge/latestdoi/51161341)
[![](https://travis-ci.org/nlpie/biomedicus.svg?branch=master)](https://travis-ci.org/nlpie/biomedicus)

# BioMedICUS (Old)
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](https://nlpie.github.io/) 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.

### Project Goals
- Scalability and performance. We use BioMedICUS to process millions of notes here at the 
University of Minnesota. To do this we need BioMedICUS to have high throughput and to support both 
machine-level and distributed parallelization. 
- Usability. We try to minimize dependencies and prerequisites that BioMedICUS requires. We release 
under the permissive Apache 2.0 license and pay close attention to intellectual property issues.

To see what tasks the system supports, look at 
[Components and Outputs](https://github.com/nlpie/biomedicus/wiki/Components-and-Outputs). If you are 
looking for a jumping-in point, see 
[Installation](https://github.com/nlpie/biomedicus/wiki/Installation).

## Features
### RTF Reader
BioMedICUS has an 
[RTF Reader](https://github.com/nlpie/biomedicus/wiki/Components-and-Outputs#rtf-pipeline), 
which has the ability to read and process notes that are encoding in RTF. In addition, BioMedICUS 
uses RTF formatting information downstream to improve other components.

### Acronym Detection
Included in the standard pipeline is an 
[acronym detector](https://github.com/nlpie/biomedicus/wiki/Components-and-Outputs#acronyms), 
which has the ability to detect and expand acronyms to their equivalent long forms.

### Concept Detection
BioMedICUS includes a fast 
[concept detector](https://github.com/nlpie/biomedicus/wiki/Components-and-Outputs#concepts) 
which labels instances of UMLS Metathesaurus concepts in text.

## Downloads
For downloads see the [releases page](https://github.com/nlpie/biomedicus/releases) on GitHub. We 
also make more comprehensive models that require you to have a UMLS license available 
[here](http://athena.ahc.umn.edu/biomedicus-downloads/).

## Wiki
[Our wiki on GitHub](https://github.com/nlpie/biomedicus/wiki) contains information about 
installation, configuration, use, and development of BioMedICUS.

## Contact and Support
For issues or enhancement requests, feel free to submit to the Issues tab on GitHub.

BioMedICUS has a [gitter chat](https://gitter.im/biomedicus/biomedicus) for contacting developers 
with questions, suggestions or feedback.

## About Us
BioMedICUS is developed by the
[University of Minnesota Institute for Health Informatics NLP/IE Group](http://www.bmhi.umn.edu/ihi/research/nlpie/)
with assistance from the
[Open Health Natural Language Processing \(OHNLP\) Consortium](http://ohnlp.org/index.php/Main_Page).

## Other Resources
### NLP-TAB
 *   [Demo](http://athena.ahc.umn.edu/nlptab)
 *   [Java Source Code](https://github.org/nlpie/nlptab)
 *   [Web-app Source Code](https://github.org/nlpie/nlptab-webapp)
 *   [Corpus](https://github.org/nlpie/nlptab-corpus)

### NLP/IE Group Resources
 *   [Website](http://www.bmhi.umn.edu/ihi/research/nlpie/resources/index.htm)
 *   [Demos](http://athena.ahc.umn.edu/)

## Acknowledgements
Funding for this work was provided by:
 *	1 R01 LM011364-01 NIH-NLM
 *	1 R01 GM102282-01A1 NIH-NIGMS
 *	U54 RR026066-01A2 NIH-NCRR

The following people have made code contributions not represented in the commit history:
 *  Robert Bill
 *  Arun Kumar
 *  Serguei Pakhomov
 *  Yan Wang

biomedicus2

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