ARC v2.0 Popular

code.google.com/p/mavericarc/

You Know About NLP If you are familiar with NLP and you are using information retrieval techniques to conduct research then you can use ARC by adding it to your existing toolkit so that it can help you get relevant data to your clinicians faster. You Ar ...

BADREX: Biomedical Abbreviation Expander with Dynamic Regular Expressions

github.com/philgooch/BADREX-Biomedical-Abbreviation-Expander

BADREX uses dynamically generated regular expressions to annotate term definition–term abbreviation pairs, and corefers unpaired acronyms and abbreviations back to their initial (or most recent) definition in the text. BADREX achieves precision and recall ...

sites.google.com/site/fmchowdhury2/bioenex

BioEnEx is a tool designed to annotate multiple biomedical entity types (i.e. genes/proteins, diseases, species, chemicals, etc) with high performance. It uses a first order CRF classifier. Separate feature sets are used for diseases and genes/proteins. F ...

BioSimplify Popular

sourceforge.net/projects/biosimplify/

BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving ...

sourceforge.net/projects/cksauthorer

Work in progress of Dr. Jonnalagadda's K99/R00 project at Mayo Clinic and Northwestern University: The use of clinical knowledge systems such as UpToDate that provide reliable information at the point of care has been shown to improve patient safety and ...

eHOST: The Extensible Human Oracle Suite of Tools

code.google.com/p/ehost/

A prototype annotation system that provides an open-source stand-alone client for manual annotation of clinical texts. The eHOST annotation tool has been used by several institutions and projects for a variety of tasks, including both the 2010 and 2011 i ...

idash.ucsd.edu/nlp/umls-vm

This virtual machine is built using VirtualBox and contains the following clinical NLP applications: 1) eHOST - an annotation tool 2) CTAKES - a clinical information extraction tool 3) ARC - automated retrieval console for creating document classifiers ...

sourceforge.net/projects/ohnlp/files/icTAKES/

Integrated cTAKES (icTAKES) is an integrated version of Mayo clinical Text Analysis and Knowledge Extraction System. We reorganized from original cTAKES to fully take advantage of the UIMA framework and allow end users and developers to set up clinical na ...

Kleio Popular

www.nactem.ac.uk/Kleio/

By combining a selection of our software services Kleio can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically ...

Lancet Popular

Lancet

code.google.com/p/lancet/

 Lancet is a supervised machine-learning system that automatically extracts medication events consisting of medication names and information pertaining to their prescribed use (dosage, mode, frequency, duration and reason) from lists or narrative text in ...

ii.nlm.nih.gov/MTI/index.shtml

The Medical Text Indexer (MTI) system was developed as part of the U. S. National Library of Medicine’s (NLM) Indexing Initiative. MTI produces both semi- and fully-automated indexing recommendations based on the Medical Subject Headings (MeSH®) controlle ...

MetaCoDe Popular

www.semantic-valley.org

MetaCoDe is currently being developped. It is another UMLS concepts extractor implemented as a GATE plugin. The purpose is to provide tagging tools available for languages other than English, the ongoing efforts being on French.

metamap.nlm.nih.gov/JavaApi.shtml

MetaMap maps terms occurring in text to UMLS Metathesaurus concepts. As part of this mapping process, MetaMap tokenizes text into sentences, phrases, and words. MetaMap maps the noun phrases of the text to the best matching UMLS concept or set of concepts ...

gate.ac.uk

MetaMap, from the National Library of Medicine (NLM), maps biomedical text to the UMLS Metathesaurus and allows Metathesaurus concepts to be discovered in a text corpus. The Tagger_MetaMap plugin for GATE wraps the MetaMap Java API client to allow GATE ...

metamap.nlm.nih.gov/UIMA.shtml

This annotator encodes MetaMap named entities in a format utilizable by UIMA components. The annotator is based on the MetaMap UIMA Wrapper (http://sourceforge.net/projects/metamap-uima/) authored by Kai Schlamp. Please Note: The MetaMap UIMA Annotator r ...

PubMed-EX Popular

code.google.com/p/pubmed-ex/

PubMed-EX is a browser extension that marks up PubMed search results with additional information retrieved from IASL & IISR text-mining services. PubMed-EX's page mark-up includes section categorization, gene/disease name, and relation. The mark-ups o ...

RapTAT - A Rapid Text Annotation Tool

code.google.com/p/raptat/

RapTAT is a Java-based tool designed to identify and optimize machine-learning methods for accelerating and/or automating free-text annotation. In the initial version of the tool, the user will train the machine-learning system by loading it with document ...

SenseClusters Popular

senseclusters.sourceforge.net

SenseClusters is a suite of Perl programs that supports unsupervised clustering of similar contexts. It relies on it's own native methodology, and also provides support for Latent Semantic Analysis. SenseClusters is a complete system that takes users from ...

The Arrowsmith Project Home Page

arrowsmith.psych.uic.edu

 Arrowsmith Two Node Search tool,  Anne O'Tate value-added PubMed search tool,  Author-ity Author Name Disambiguation tools, ADAM abbreviation database,    WETLAB prototype electronic lab notebook,   Compendium of Biomedical Text Mining tools,   ...

U-Compare Popular

www.nactem.ac.uk/u-compare.php

U-Compare is an integrated text mining/natural language processing system based on the UIMA Framework, which provides access to a large collection of ready-to-use interoperable natural language processing components, currently the world's largest UIMA com ...