title: The GNAT library for local and remote gene mention normalization.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  The library and web services are implemented in Java and the sources are available from http://gnat.sourceforge.net.
  
  
  BACKGROUND
  jorg.hakenberg@roche.com.
authors.affiliation: Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA. jorg.hakenberg@roche.com
authors.forename: Jörg
authors.initials: J
authors.lastname: Hakenberg
authors.forename: Martin
authors.initials: M
authors.lastname: Gerner
authors.forename: Maximilian
authors.initials: M
authors.lastname: Haeussler
authors.forename: Illés
authors.initials: I
authors.lastname: Solt
authors.forename: Conrad
authors.initials: C
authors.lastname: Plake
authors.forename: Michael
authors.initials: M
authors.lastname: Schroeder
authors.forename: Graciela
authors.initials: G
authors.lastname: Gonzalez
authors.forename: Goran
authors.initials: G
authors.lastname: Nenadic
authors.forename: Casey M
authors.initials: CM
authors.lastname: Bergman
mesh_terms: D057225:Data Mining; D001330:Electronic Data Processing; D015723:Gene Library; D005796:Genes; D020407:Internet; D011506:Proteins; D011643:Publishing; D009626:Terminology as Topic
chemical_list: D011506:Proteins