Sonya

Word sense ambiguity is a pervasive characteristic of natural language. For example, the word "cold" has several senses and may refer to a disease, a temperature sensation, or an environmental condition. The specific sense intended is determined by the te ...

Category Structured Data

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 ...

ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the int ...

The "PK DDI" corpus is a new corpus of sections from FDA-approved drug  package inserts (PIs) that have been manually annotated for  pharmacokinetic drug-drug interactions by a pharmacist and a drug  information expert. The two annotators reached consensu ...

Category Human Annotated

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).

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

The RxNorm API is a web service for accessing the current RxNorm data set from your program. Clients can access the web service via SOAP/WSDL or through a RESTful interface. RxNorm provides normalized names for clinical drugs and links its names to many o ...

Category Bioinformatics

RxNorm, a standardized nomenclature for clinical drugs and drug delivery devices, is produced by the National Library of Medicine (NLM). In this context, a clinical drug is a pharmaceutical product given to (or taken by) a patient with a therapeutic or di ...

Category Structured Data

RxNav is a browser for several drug information sources, including RxNorm, RxTerms and NDF-RT. RxNav finds drugs in RxNorm from the names and codes in its constituent vocabularies. RxNav displays links from clinical drugs, both branded and generic, to the ...

Category Bioinformatics
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 ...

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 ...

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 ...

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
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

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

The NDF-RT API is a web service for accessing the current National Drug File - Reference Terminology (NDF-RT) data set from your program via SOAP/WSDL or through a RESTful interface.  The NDF-RT RESTful web API is a simple web service implemented using HT ...

Category Bioinformatics

The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL s ...

Category Bioinformatics

This package provides machine learning algorithms optimized for large text categorization tasks and is able to combine several text categorization solutions. The advantages of this package compared to existing approaches are: 1) its speed, 2) it is able t ...

MsPI is a software tool for protein identification from PMF data. It can be downloaded freely for non-profit institutions from http://aimed11.unipv.it/MsPI

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 ...