Overview of BioCreative II gene mention recognition

Larry Smith, Lorraine K. Tanabe, Rie Ando, Cheng Ju Kuo, I. Fang Chung, Chun Nan Hsu, Yu Shi Lin, Roman Klinger, Christoph M. Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu, Barry Haddow, Craig A. Struble, Richard J. Povinelli, Andreas Vlachos, William A. Baumgartner, Lawrence Hunter, Bob Carpenter, Richard Tzong Han TsaiHong Jie Dai, Feng Liu, Yifei Chen, Chengjie Sun, Sophia Katrenko, Pieter Adriaans, Christian Blaschke, Rafael Torres, Mariana Neves, Preslav Nakov, Anna Divoli, Manuel Maña-López, Jacinto Mata, W. John Wilbur

Research output: Contribution to journalArticle

186 Citations (Scopus)

Abstract

Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.

Original languageEnglish
Article numberS2
JournalGenome Biology
Volume9
Issue numberSUPPL. 2
DOIs
Publication statusPublished - 1 Sep 2008
Externally publishedYes

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gene
Genes
Names
statistical analysis
genes
Education
methodology
method

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Smith, L., Tanabe, L. K., Ando, R., Kuo, C. J., Chung, I. F., Hsu, C. N., ... Wilbur, W. J. (2008). Overview of BioCreative II gene mention recognition. Genome Biology, 9(SUPPL. 2), [S2]. https://doi.org/10.1186/gb-2008-9-s2-s2

Overview of BioCreative II gene mention recognition. / Smith, Larry; Tanabe, Lorraine K.; Ando, Rie; Kuo, Cheng Ju; Chung, I. Fang; Hsu, Chun Nan; Lin, Yu Shi; Klinger, Roman; Friedrich, Christoph M.; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A.; Povinelli, Richard J.; Vlachos, Andreas; Baumgartner, William A.; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong Han; Dai, Hong Jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres, Rafael; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Maña-López, Manuel; Mata, Jacinto; Wilbur, W. John.

In: Genome Biology, Vol. 9, No. SUPPL. 2, S2, 01.09.2008.

Research output: Contribution to journalArticle

Smith, L, Tanabe, LK, Ando, R, Kuo, CJ, Chung, IF, Hsu, CN, Lin, YS, Klinger, R, Friedrich, CM, Ganchev, K, Torii, M, Liu, H, Haddow, B, Struble, CA, Povinelli, RJ, Vlachos, A, Baumgartner, WA, Hunter, L, Carpenter, B, Tsai, RTH, Dai, HJ, Liu, F, Chen, Y, Sun, C, Katrenko, S, Adriaans, P, Blaschke, C, Torres, R, Neves, M, Nakov, P, Divoli, A, Maña-López, M, Mata, J & Wilbur, WJ 2008, 'Overview of BioCreative II gene mention recognition', Genome Biology, vol. 9, no. SUPPL. 2, S2. https://doi.org/10.1186/gb-2008-9-s2-s2
Smith L, Tanabe LK, Ando R, Kuo CJ, Chung IF, Hsu CN et al. Overview of BioCreative II gene mention recognition. Genome Biology. 2008 Sep 1;9(SUPPL. 2). S2. https://doi.org/10.1186/gb-2008-9-s2-s2
Smith, Larry ; Tanabe, Lorraine K. ; Ando, Rie ; Kuo, Cheng Ju ; Chung, I. Fang ; Hsu, Chun Nan ; Lin, Yu Shi ; Klinger, Roman ; Friedrich, Christoph M. ; Ganchev, Kuzman ; Torii, Manabu ; Liu, Hongfang ; Haddow, Barry ; Struble, Craig A. ; Povinelli, Richard J. ; Vlachos, Andreas ; Baumgartner, William A. ; Hunter, Lawrence ; Carpenter, Bob ; Tsai, Richard Tzong Han ; Dai, Hong Jie ; Liu, Feng ; Chen, Yifei ; Sun, Chengjie ; Katrenko, Sophia ; Adriaans, Pieter ; Blaschke, Christian ; Torres, Rafael ; Neves, Mariana ; Nakov, Preslav ; Divoli, Anna ; Maña-López, Manuel ; Mata, Jacinto ; Wilbur, W. John. / Overview of BioCreative II gene mention recognition. In: Genome Biology. 2008 ; Vol. 9, No. SUPPL. 2.
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