Tags: NLP - information extraction

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 ...

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 ...

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 ...

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 ...

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 ...

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

 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 ...

LingPipe Text Analytics Java API

LingPipe is tool kit for processing text using computational linguistics. LingPipe is used to do tasks like: Find the names of people, organizations or locations in news Automatically classify Twitter search results into categories Suggest correct sp ...

Category Sectionizer

LingScope detects scope of negation and hedging in biomedical and clinical literature.

The LONI Pipeline is a visual language  programming environment  for study designs and data provenance based on complex graphical  workflows. The construction, validation and dissemination of study designs via the  LONI Pipeline uses advanced neuroimaging ...

Category Bioinformatics
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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 ...

MERKI extracts patient medication information from structured and free-text clinical data sources. The extracted medication information can be used for medication reconciliation, harmacovigilance and quality assurance. MERKI outputs medication information ...

MetaMap is a highly configurable application developed by the Lister Hill National Center for Biomedical Communications at the National Library of Medicine (NLM) to map biomedical text to the UMLS Metathesaurus or, equivalently, to identify Metathesaurus ...