A multistage gene normalization system integrating multiple effective methods

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Li, Lishuang ^a   Liu, Shanshan ^a   Li, Lihua ^b   Fan, Wenting ^a   Huang, Degen ^a   Zhou, Huiwei ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b HEBEI NORMAL UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BOOK; FILTRATION; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MULTIGENE FAMILY; MULTISTAGE GENE NORMALIZATION SYSTEM; PROTEIN FAMILY; SCORING SYSTEM; SYSTEMATIC ERROR;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA MINING; GENES; HUMANS; MOLECULAR SEQUENCE ANNOTATION; SEMANTICS;

EID: 84892602367     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081956     Document Type: Article

References (17)

1. Morgan AA, Lu ZY, Wang XL, Cohen AM, Fluck J, et al. (2008) Overview of BioCreative gene normalization. Genome Biology 9: S3.
2. Hakenberg J, Royer L, Plake C, Strobelt H, Schroeder M (2007) Me and my friends: gene mention normalization with background knowledge. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop. Madrid, Spain, pp. 141-144.
3. Neves ML, Carazo JM, Alberto PM (2010) Moara: a java library for extracting and normalizing gene and protein mentions. BMC Bioinformatics 11: 157.
4. Xia N, Lin HF, Yang ZH, Li YP (2011) Combining multiple disambiguation methods for gene mention normalization. Expert Systems with Applications 38: 7994-7999.
5. Wermter J, Tomanek K, Hahn U (2009) High-performance gene name normalization with geno. Bioinformatics 25: 815-821.
6. Liu H, Torii M, Hu ZZ, Wu C (2007) Gene mention and gene normalization based on machine learning and online resources. In: Madrid, Spain, Proceedings of the Second BioCreative Challenge Evaluation Workshop. pp. 135-140.
7. Lau W, Johnson C (2007) Rule-based human gene normalization in biomedical text with confidence estimation. In: Madrid, Spain, Proceedings of the Second BioCreative Challenge Evaluation Workshop. pp. 165-168.
8. Gonzalez G, Tari L, Gitter A, Leaman R, Nikkila S (2007) Integrating knowledge from biomedical literature. In: Madrid, Spain, Proceedings of the Second BioCreative Challenge Evaluation Workshop. pp. 227-236.
9. Grover C, Haddow B, Klein E, Matthews M, Neilsen L, et al. (2007) Adapting a relation extraction pipeline for the BioCreAtIvE II task. In: Madrid, Spain, Proceedings of the BioCreAtIvE II Workshop. pp. 273-286.
10. Huang M, Liu J, Zhu X (2011) Genetukit: a software for document-level gene normalization. Bioinformatics 27: 1032-1033.
11. Hakenberg J, Plake C, Royer L, Strobelt H, Leser U, et al. (2008) Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biology 9: S14.
12. Hu Y, Li Y, Lin H, Yang Z, Cheng L (2012) Integrating various resources for gene name normalization. PLOS ONE 7: e43558.
13. Li LS, Fan WT, Huang DG, Dang YZ, Sun J (2012) Boosting performance of gene mention tagging system by hybrid methods. Journal of Biomedical Informatics 45: 156-164.
14. Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, et al. (2008) Overview of BioCreative gene mention recognition. Genome Biology 9: S2.
15. The defination of gene-family in Wikipedia. Available. http://en.wikipedia.org/wiki/Gene-family. Accessed 2013 August 1.
16. Munkres' assignment algorithm. Available. http://csclab.murraystate.edu/ bob.pilgrim/445/munkres.html. Accessed 2010 Jun 3.
17. The Protein family term of Wikipedia. Available. http://en.wikipedia.org/ wiki/Category:Protein-families. Accessed 2013 March 30.