GNAT library for local and remote gene mention normalization

• Published in: Bioinformatics 2011-10, Vol.27 (19), p.2769-2771
• Main Authors: Hakenberg, Jörg, Gerner, Martin, Haeussler, Maximilian, Solt, Illés, Plake, Conrad, Schroeder, Michael, Gonzalez, Graciela, Nenadic, Goran, Bergman, Casey M
• Format: Article
• Language: English
• Subjects: Applications Note; Automatic Data Processing; Bioinformatics; Biological and medical sciences; Data Mining; Fundamental and applied biological sciences. Psychology; Gene Library; General aspects; Genes; information retrieval; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Proteins; Publishing; Terminology as Topic
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btr455

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: [e-mail]