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BioMedICUS

The BioMedical Information Collection and Understanding System (BioMedICUS) is a system for large-scale text analysis and processing of biomedical and clinical reports.

License

License
GroupId

GroupId

edu.umn.biomedicus
ArtifactId

ArtifactId

biomedicus
Last Version

Last Version

2.1.0
Release Date

Release Date
Type

Type

pom
Description

Description

BioMedICUS
The BioMedical Information Collection and Understanding System (BioMedICUS) is a system for large-scale text analysis and processing of biomedical and clinical reports.
Project URL

Project URL

https://nlpie.github.io/biomedicus
Project Organization

Project Organization

University of Minnesota Institute for Health Informatics NLP/IE Program
Source Code Management

Source Code Management

https://github.com/NLPIE/BioMedICUS

Download biomedicus

Filename Size
biomedicus-2.1.0.pom 12 KB
Browse

How to add to project

<!-- https://jarcasting.com/artifacts/edu.umn.biomedicus/biomedicus/ -->
<dependency>
    <groupId>edu.umn.biomedicus</groupId>
    <artifactId>biomedicus</artifactId>
    <version>2.1.0</version>
    <type>pom</type>
</dependency>
// https://jarcasting.com/artifacts/edu.umn.biomedicus/biomedicus/
implementation 'edu.umn.biomedicus:biomedicus:2.1.0'
// https://jarcasting.com/artifacts/edu.umn.biomedicus/biomedicus/
implementation ("edu.umn.biomedicus:biomedicus:2.1.0")
'edu.umn.biomedicus:biomedicus:pom:2.1.0'
<dependency org="edu.umn.biomedicus" name="biomedicus" rev="2.1.0">
  <artifact name="biomedicus" type="pom" />
</dependency>
@Grapes(
@Grab(group='edu.umn.biomedicus', module='biomedicus', version='2.1.0')
)
libraryDependencies += "edu.umn.biomedicus" % "biomedicus" % "2.1.0"
[edu.umn.biomedicus/biomedicus "2.1.0"]

Dependencies

compile (4)

Group / Artifact Type Version
org.jetbrains.kotlin : kotlin-stdlib-jdk8 jar 1.3.11
org.jetbrains.kotlin : kotlin-reflect jar 1.3.11
org.slf4j : slf4j-api jar 1.7.25
com.google.code.findbugs : jsr305 Optional jar 3.0.2

test (5)

Group / Artifact Type Version
org.jetbrains.kotlin : kotlin-test-junit5 jar 1.3.11
com.nhaarman.mockitokotlin2 : mockito-kotlin jar 2.1.0
org.junit.jupiter : junit-jupiter-engine jar 5.3.2
org.mockito : mockito-core jar 2.23.4
org.slf4j : slf4j-nop jar 1.7.25

Project Modules

  • biomedicus-core
  • biomedicus-rtf
  • biomedicus-uima
  • biomedicus-distribution
  • nlpengine

New Version

BioMedICUS has a new version: https://github.com/nlpie/biomedicus3

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

























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 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. If you are looking for a jumping-in point, see Installation.

Features

RTF Reader

BioMedICUS has an RTF Reader, 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, which has the ability to detect and expand acronyms to their equivalent long forms.

Concept Detection

BioMedICUS includes a fast concept detector which labels instances of UMLS Metathesaurus concepts in text.

Downloads

For downloads see the releases page on GitHub. We also make more comprehensive models that require you to have a UMLS license available here.

Wiki

Our wiki on GitHub 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 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 with assistance from the Open Health Natural Language Processing (OHNLP) Consortium.

Other Resources

NLP-TAB

NLP/IE Group Resources

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
edu.umn.biomedicus

Natural Language Processing / Information Extraction (NLP/IE) Program

The Natural Language Processing / Information Extraction (NLP/IE) Program at the University of Minnesota Institute for Health Informatics

Versions

Version
2.1.0
2.0.1
2.0.0