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The GNAT library for local and remote gene mention normalization.

Hakenberg, Jörg; Gerner, Martin; Haeussler, Maximilian; Solt, Illés; Plake, Conrad; Schroeder, Michael; Gonzalez, Graciela; Nenadic, Goran; Bergman, Casey M

Bioinformatics (Oxford, England). 2011;27(19):2769-2771.

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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.

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Type of resource:
Content type:
Publication type:
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Volume:
27
Issue:
19
Pagination:
2769-2771
Digital Object Identifier:
10.1093/bioinformatics/btr455
Pubmed Identifier:
21813477
Pii Identifier:
btr455
Access state:
Active

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Record metadata

Manchester eScholar ID:
uk-ac-man-scw:132781
Created by:
Bergman, Casey
Created:
10th October, 2011, 14:41:43
Last modified by:
Bergman, Casey
Last modified:
6th March, 2016, 19:30:59

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