title: BioTagger-GM: a gene/protein name recognition system.
abstract: OBJECTIVE
  Biomedical named entity recognition (BNER) is a critical component in automated systems that mine biomedical knowledge in free text. Among different types of entities in the domain, gene/protein would be the most studied one for BNER. Our goal is to develop a gene/protein name recognition system BioTagger-GM that exploits rich information in terminology sources using powerful machine learning frameworks and system combination.
  
  
  METHODS
  BioTagger-GM consists of four main components: (1) dictionary lookup-gene/protein names in BioThesaurus and biomedical terms in UMLS Metathesaurus are tagged in text, (2) machine learning-machine learning systems are trained using dictionary lookup results as one type of feature, (3) post-processing-heuristic rules are used to correct recognition errors, and (4) system combination-a voting scheme is used to combine recognition results from multiple systems.
  
  
  METHODS
  The BioCreAtIvE II Gene Mention (GM) corpus was used to evaluate the proposed method. To test its general applicability, the method was also evaluated on the JNLPBA corpus modified for gene/protein name recognition. The performance of the systems was evaluated through cross-validation tests and measured using precision, recall, and F-Measure.
  
  
  RESULTS
  BioTagger-GM achieved an F-Measure of 0.8887 on the BioCreAtIvE II GM corpus, which is higher than that of the first-place system in the BioCreAtIvE II challenge. The applicability of the method was also confirmed on the modified JNLPBA corpus.
  
  
  CONCLUSIONS
  The results suggest that terminology sources, powerful machine learning frameworks, and system combination can be integrated to build an effective BNER system.
authors.affiliation: The Imaging Science and Information Systems Center, Department of Oncology, Georgetown University Medical Center, 2115 Wisconsin Avenue NW, Washington, DC 20057, USA. torii@isis.georgetown.edu
authors.forename: Manabu
authors.initials: M
authors.lastname: Torii
authors.forename: Zhangzhi
authors.initials: Z
authors.lastname: Hu
authors.forename: Cathy H
authors.initials: CH
authors.lastname: Wu
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
mesh_terms: D001185:Artificial Intelligence; D030541:Databases, Genetic; D005796:Genes; D011506:Proteins / Q000235:genetics; D017432:Unified Medical Language System
chemical_list: D011506:Proteins