Tags: Text mining

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 ...

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 ...

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 ...

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 ...

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

MALLET is a Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to text. MALLET includes sophisticated tools for document cla ...

Category Classification

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 ...

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, 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 ...

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 ...

NEMO is developed to associate each biomedical paper and its authors with a unique organization name and the geopolitical location of that organization. This system provides more accurate information about organizations than the raw affiliation strings pr ...

Category Text Mining
Neuroscience Information Framework (NIF)

Informatics and new web technologies (e.g. ontologies, social networking and community wikis) are becoming increasingly important to biomedical researchers. The sharing of research data and information pertaining to resources (i.e. tools, data, materials ...

Category Annotation

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 ...

QuExT (Query Expansion Tool) is a webserver designed to aid researchers working with large datasets find relationships between genes. It works through expanding each gene name into several associated terms, such as protein products of gene translation, me ...

RapidMiner is an environment for machine learning and data mining experiments. It allows experiments to be made up of a large number of arbitrarily nestable operators, described in XML files which are created with RapidMiner's graphical user interface. Ra ...

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 ...