Tags: NLP - Information extraction

The purpose of NLM's Unified Medical Language System® (UMLS) is to facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health. To that end, NLM produces and distributes the UMLS ...

This package consists of Perl modules along with supporting Perl programs that implement the semantic similarity and relatedness measures described by Leacock & Chodorow (1998), Wu & Palmer (1994), Nguyen and Al-Mubaid (2006), Rada, et. al. 1989, ...

This package provides a Perl interface to the Unified Medical Language System (UMLS). The UMLS is a knowledge representation framework encoded designed to support broad scope biomedical research queries. There exists three major sources in the UMLS. The M ...

UMLS Visualizer

This is a link to a java based UMLS visualizer. Your comments are most welcome.  It takes 30-60 seconds to load when first invoked.  Instructions:  Select the databases to search on the right. Type in a particular term at the bottom and press return.  Th ...

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 ...

The MITRE Identification Scrubber Toolkit (MIST) is a suite of tools for identifying and redacting personally identifiable information (PII) in free-text medical records. MIST helps you replace these PII either with obscuring fillers, such as [NAME], or w ...

The Arrowsmith Project Home Page

 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,   ...

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 ...

SemRep is a program that extracts semantic predications (subject-predicate-object triples) from biomedical free text. Elements of a semantic predications are drawn from the UMLS knowledge sources; the subject and object pair corresponds to UMLS Metathesau ...

SecTag

Clinical notes are often divided into sections, or segments, such as "history of present illness" or "past medical history." These sections often have subsections as well, such as the "cardiovascular exam" section of the "physical exam." One can gain grea ...

Category Sectionizer
RapTAT - A Rapid Text Annotation Tool

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 ...

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 ...

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 ...

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 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 ...

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 ...

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 ...

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 ...

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