Tags: Named entity recognition

The Yale cTAKES Extensions (YTEX) is a set of UIMA annotation engines and utilites that complement the Clinical Text Analysis and Knowledge Extraction System (cTAKES). These include: Semantic Search Engine: A web service that enables users to find doc ...

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 ...

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 ...

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 ...

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 ...

NER-based semantic classifier for diseases in discharge summaries

The system performs identification of disease mentions in discharge summaries also assessing uncertainty and negation. Evaluated at the i2b2 Obesity Challenge ranking 1st and 2nd in the textual (explicit) and intuitive (implicit) subtasks respectively. ...

Category Sectionizer

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 ...

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

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 ...

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 ...

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). ...