title: GeneTUKit: a software for document-level gene normalization.
abstract: BACKGROUND
  Linking gene mentions in an article to entries of biological databases can facilitate indexing and querying biological literature greatly. Due to the high ambiguity of gene names, this task is particularly challenging. Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value.
  
  
  RESULTS
  We developed GeneTUKit, a document-level gene normalization software for full-text articles. This software employs both local context surrounding gene mentions and global context from the whole full-text document. It can normalize genes of different species simultaneously. When participating in BioCreAtIvE III, the system obtained good results among 37 runs: the system was ranked first, fourth and seventh in terms of TAP-20, TAP-10 and TAP-5, respectively on the 507 full-text test articles.
  
  
  METHODS
  The software is available at http://www.qanswers.net/GeneTUKit/.
authors.affiliation: Department of Computer Science and Technology, Tsinghua University, Beijing, China. aihuang@tsinghua.edu.cn
authors.forename: Minlie
authors.initials: M
authors.lastname: Huang
authors.forename: Jingchen
authors.initials: J
authors.lastname: Liu
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Zhu
mesh_terms: D057225:Data Mining; D005796:Genes; D012016:Reference Values; D012984:Software