Overview of BioCreative II gene mention recognition

被引：252

作者：

Smith, Larry ^{[1
]}

Tanabe, Lorraine K. ^{[1
]}

Johnson Nee Ando, Rie ^{[2
]}

Kuo, Cheng-Ju ^{[3
]}

Chung, I-Fang ^{[3
]}

Hsu, Chun-Nan ^{[4
]}

Lin, Yu-Shi ^{[4
]}

Klinger, Roman ^{[5
]}

Friedrich, Christoph M. ^{[5
]}

Ganchev, Kuzman ^{[6
]}

Torii, Manabu ^{[7
]}

Liu, Hongfang ^{[7
]}

Haddow, Barry ^{[8
]}

Struble, Craig A. ^{[9
]}

Povinelli, Richard J. ^{[10
]}

Vlachos, Andreas ^{[11
]}

Baumgartner, William A., Jr. ^{[12
]}

Hunter, Lawrence ^{[12
]}

Carpenter, Bob ^{[13
]}

Tsai, Richard Tzong-Han ^{[4
,14
]}

Dai, Hong-Jie ^{[4
,15
]}

Liu, Feng ^{[16
]}

Chen, Yifei ^{[16
]}

Sun, Chengjie ^{[17
]}

Katrenko, Sophia ^{[18
]}

Adriaans, Pieter ^{[18
]}

Blaschke, Christian ^{[19
]}

Torres, Rafael ^{[19
]}

Neves, Mariana ^{[20
]}

Nakov, Preslav ^{[21
,22
]}

Divoli, Anna ^{[23
]}

Mana-Lopez, Manuel ^{[24
]}

Mata, Jacinto ^{[24
]}

Wilbur, W. John ^{[1
]}

机构：

[1] Natl Lib Med, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA

[2] IBM TJ Watson Res Ctr, Yorktown Hts, NY USA

[3] Natl Yang Ming Univ, Inst Bioinformat, Taipei 112, Taiwan

[4] Acad Sinica, Inst Informat Sci, Taipei, Taiwan

[5] Fraunhofer Inst Algorithms & Sci Comp, Dept Bioinformat, Schloss Birlinghoven, Sankt Augustin, Germany

[6] Univ Penn, Dept Comp & Informat Sci, Philadelphia, PA 19104 USA

[7] Georgetown Univ, Med Ctr, Dept Biostat Bioinformat & Biomath, Washington, DC 20007 USA

[8] Univ Edinburgh, Sch Informat, Edinburgh EH8 9YL, Midlothian, Scotland

[9] Marquette Univ, Dept Math Stat & Comp Sci, Milwaukee, WI 53233 USA

[10] Marquette Univ, Dept Elect & Comp Engn, Milwaukee, WI 53233 USA

[11] Univ Cambridge, Comp Lab, Cambridge CB2 3QG, England

[12] Univ Colorado, Sch Med, Ctr Computat Pharmacol, Denver, CO USA

[13] Alias I Inc, Brooklyn, NY USA

[14] Yuan Ze Univ, Dept Comp Sci & Engn, Tao Yuan, Taiwan

[15] Natl Tsing Hua Univ, Dept Comp Sci, Hsinchu 30043, Taiwan

[16] Vrije Univ Brussels, Computat Modeling Lab, Brussels, Belgium

[17] Harbin Inst Technol, Sch Comp Sci & Technol, Harbin 150006, Peoples R China

[18] Univ Amsterdam, Inst Informat, Human Comp Studies Lab, Amsterdam, Netherlands

[19] Bioalma, Madrid, Spain

[20] Univ Complutense Madrid, Fac Informat, Madrid, Spain

[21] Univ Calif Berkeley, Dept Elect Engn & Comp Sci, Div Comp Sci, Berkeley, CA 94720 USA

[22] Bulgarian Acad Sci, Inst Parallel Proc, Linguist Modeling Dept, Sofia, Bulgaria

[23] Univ Calif Berkeley, Sch Informat, Berkeley, CA 94720 USA

[24] Univ Huelva, Dept Tecnol Informac, Huelva, Spain

来源：

GENOME BIOLOGY | 2008年 / 9卷

关键词：

D O I：

10.1186/gb-2008-9-S2-S2

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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 F-1 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.

引用

页数：19

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