title: A multistage gene normalization system integrating multiple effective methods.
abstract: Gene/protein recognition and normalization is an important preliminary step for many biological text mining tasks. In this paper, we present a multistage gene normalization system which consists of four major subtasks: pre-processing, dictionary matching, ambiguity resolution and filtering. For the first subtask, we apply the gene mention tagger developed in our earlier work, which achieves an F-score of 88.42% on the BioCreative II GM testing set. In the stage of dictionary matching, the exact matching and approximate matching between gene names and the EntrezGene lexicon have been combined. For the ambiguity resolution subtask, we propose a semantic similarity disambiguation method based on Munkres' Assignment Algorithm. At the last step, a filter based on Wikipedia has been built to remove the false positives. Experimental results show that the presented system can achieve an F-score of 90.1%, outperforming most of the state-of-the-art systems.
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China.
authors.forename: Lishuang
authors.initials: L
authors.lastname: Li
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Liu
authors.affiliation: School of Mathmatics and Information Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Li
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China.
authors.forename: Wenting
authors.initials: W
authors.lastname: Fan
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China.
authors.forename: Degen
authors.initials: D
authors.lastname: Huang
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China.
authors.forename: Huiwei
authors.initials: H
authors.lastname: Zhou
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000706:statistics & numerical data*; D005796:Genes; D006801:Humans; D058977:Molecular Sequence Annotation / Q000592:standards*; D012660:Semantics