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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 ...

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 ...

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
E-mail

This site, established by Bob Futrelle in January 2001, is to be a collection of resources and links to resources about all aspects of natural language processing (NLP) and in particular its use in information extraction from biology texts. It is a non-co ...

Category Online Community

Pentaho Data Integration, codenamed Kettle, consists of a core data integration engine, and GUI applications that allow the user to define data integration jobs and transformations. It supports deployment on single node computers as well as on a cloud, or ...

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 ...

NeuroLex - A dynamic lexicon of neuroscience terms

 The NeuroLex project, supported by the Neuroscience Information Framework project, is a dynamic lexicon of neuroscience terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. The NeuroLex is being ...

Category Human Annotated
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

This corpus originated from the BioCreAtIvE task 1A data set for named entity recognition of gene/protein names. We randomly selected 1000 sentences from this set and added additional annotation for interactions between genes/proteins. 173 sentences conta ...

Category Human Annotated

  The Clinical and Translational Science Awards (CTSAs) program supports a national consortium of medical research insti-tutions designed to transform how biomedical research is conducted. Its goals are to speed the translation of laboratory disc ...

Category Online Community

See link to CMC resource catalog on upper right side of page.  All resources are fully open-access, but a registration is needed.  We simply take user and dowload counts and report back to our benifactors.  No data are shared. You will need to download t ...

Category Human Annotated
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). ...

BioInfer: Bio Information Extraction Resource

Biomedical Information Extraction Resource (BioInfer) is a public resource providing a manually annotated corpus and related resources for information extraction in the biomedical domain. The corpus contains sentences from abstracts of biomedical researc ...

Category Human Annotated

Structured abstracts contain distinct labeled sections (e.g., “RESULTS”) for key information from articles they summarize.  If English-language structured abstracts appear in journals that the US National Library of Medicine (NLM) indexes, the labels in t ...

Category Structured Data

Surveyor is a ruby gem and developer tool that enables data gathering in Rails applications. Surveys are written in the Surveyor DSL (Domain  Specific Language).

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 ...

Researchers have requested the ability to have available MEDLINE citations in the state they were at a given moment in time without the MeSH vocabulary updates and other revisions that occur during the year. The MEDLINE/PubMed Baseline Repository was set ...

Category Structured Data

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 ...

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 ...