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 "DrugDDI: an annotated corpus for drug-drug interactions" submitted for publication.   The DrugDDI corpus is part of a larger study about automatic Drug-Drug Interaction Extraction. The corpus provides data for the development and automatic evaluatio ...

Category Human Annotated

The dataset was prepared for the Genic Interaction Extraction Challenge. Extracting gene interaction means extracting the agent (proteins) and the target (genes) of all couples of genic interactions from sentences.  MIG-INRA has annotated hundreds of such ...

Category Human Annotated

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
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,   ...

Health Ontology Mapper (HOM)

The CTSA Health Ontology Mapper (HOM) is an open source general purpose instance mapper running as an i2b2 cell designed for academic research and hospital environments. It can convert locally obtained data (which may not be encoded using any nationally r ...

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 ...

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

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 ...

Lancet

 Lancet is a supervised machine-learning system that automatically extracts medication events consisting of medication names and information pertaining to their prescribed use (dosage, mode, frequency, duration and reason) from lists or narrative text in ...

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 ...

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 ...

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 ...

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 ...

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 ...

A collection of query-based summaries sourced from the Clinical Inquiries section of the Journal of Family Practice. The data are formatted in XML and are annotated with: The clinical question; The answer(s) to the question; The evidence grade of the ...

Category Human Annotated

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 ...

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 ...

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 ...

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 ...

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 ...