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ABNER

ABNER is a software tool for molecular biology text analysis. It began as a user-friendly interface for a system developed as part of the NLPBA/BioNLP 2004 Shared Task challenge. The details of that system are described in the paper below (Settles, 2004). ...

Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts. You can ...

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 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 ...

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 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 ...

brat rapid annotation tool, is a free, open-source, web-based tool for text annotation visualisation and editing. brat is fully configurable and can support a wide variety of annotation tasks, including, for example: * entity mention ("named entity") an ...

Category Annotation

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 ...

CLAMP - Clinical Language Annotation, Modeling and Processing toolkit

CLAMP is a comprehensive clinical Natural Language Processing (NLP) software that enables recognition and automatic encoding of clinical information in narrative patient reports. It provides not only state-of-the-art NLP components but also a user-friendl ...

Category Software
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CliNER

Open-source natural language processing system for named entity recognition in clinical text of electronic health records. CliNER will identify clinically-relevant entities mentioned in a clinical narrative (such as diseases/disorders, signs/symptoms, med ...

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CRC Annotators were created to support the extraction of tumor stage, TNM descriptors, lymph nodes and resection margin status from clinical notes. Prostate cancer annotators can be used to extract Gleason's score from the unstructured notes. These annota ...

ConText is based on a negation algorithm called NegEx. ConText's input is a sentence with indexed clinical conditions; ConText's output for each indexed condition is the value for contextual features or modifiers. The initial versions of ConText determine ...

Distributome

The Distributome Project is an open-source, open content-development project for exploring, discovering, learning, and computational utilization of diverse probability distributions. Probability distributions are a special class of functions defined in te ...

Category Bioinformatics

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 ...

GeneBrowser

 GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided in ...

Category Gene Expression

Harvard Catalyst Profiles is a research networking and expertise mining software tool. It not only shows traditional directory information, but also illustrates how each person is connected to others in the broad research community. As you navigate throug ...

Category Other
Health Ontology Mapper (HOM)

The CTSA Health Ontology Mapper (HOM) is an open source general purpose instance mapper running as an i2b2 cell designed for academic research and hospital environments. It can convert locally obtained data (which may not be encoded using any nationally r ...

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 ...