Sonya

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). ...

BADREX uses dynamically generated regular expressions to annotate term definition–term abbreviation pairs, and corefers unpaired acronyms and abbreviations back to their initial (or most recent) definition in the text. BADREX achieves precision and recall ...

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

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 ...

brat rapid annotation tool, is a free, open-source, web-based tool for text annotation visualisation and editing. brat is fully configurable and can support a wide variety of annotation tasks, including, for example: * entity mention ("named entity") an ...

Category Annotation

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 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
GeneBrowser

 GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided in ...

Category Gene Expression

This virtual machine is built using VirtualBox and contains the following clinical NLP applications: 1) eHOST - an annotation tool 2) CTAKES - a clinical information extraction tool 3) ARC - automated retrieval console for creating document classifiers ...

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 ...

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 ...

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 ...

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

MedlinePlus Connect allows patient portals and electronic health record (EHR) systems to use existing code sets to link to relevant, authoritative patient health information from MedlinePlus.gov. Matches ICD-9-CM or SNOMED CT CORE Problem List Subset code ...

MetaCoDe is currently being developped. It is another UMLS concepts extractor implemented as a GATE plugin. The purpose is to provide tagging tools available for languages other than English, the ongoing efforts being on French.

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 ...

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 ...

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 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 ...

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