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The GNAT library for local and remote gene mention normalization

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Item Type:Article
Title:The GNAT library for local and remote gene mention normalization
Creators Name:Hakenberg, J. and Gerner, M. and Haeussler, M. and Solt, I. and Plake, C. and Schroeder, M. and Gonzalez, G. and Nenadic, G. and Bergman, C.M.
Abstract:SUMMARY: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987. AVAILABILITY: The library and web services are implemented in Java and the sources are available from http://gnat.sourceforge.net. CONTACT: jorg.hakenberg@roche.com.
Keywords:Automatic Data Processing, Data Mining, Gene Library, Genes, Internet, Proteins, Publishing, Terminology as Topic
Source:Bioinformatics
ISSN:1367-4803
Publisher:Oxford University Press (U.K.)
Volume:27
Number:19
Page Range:2769-2771
Date:1 October 2011
Official Publication:https://doi.org/10.1093/bioinformatics/btr455
PubMed:View item in PubMed

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