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 Tsai; Hong 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

doi:10.1186/gb-2008-9-s2-s2

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

Digital Health Sciences

Research output: Contribution to journal › Review article › peer-review

221 Scopus citations

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 language	English (US)
Article number	S2
Journal	Genome biology
Volume	9
Issue number	SUPPL. 2
DOIs	https://doi.org/10.1186/gb-2008-9-s2-s2
State	Published - Sep 1 2008

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2008-9-s2-s2

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Smith, L., Tanabe, L. K., Ando, R., Kuo, C. J., Chung, I. F., Hsu, C. N., Lin, Y. S., Klinger, R., Friedrich, C. M., Ganchev, K., Torii, M., Liu, H., Haddow, B., Struble, C. A., Povinelli, R. J., Vlachos, A., Baumgartner, W. A., Hunter, L., Carpenter, B., ... Wilbur, W. J. (2008). Overview of BioCreative II gene mention recognition. Genome biology, 9(SUPPL. 2), Article S2. https://doi.org/10.1186/gb-2008-9-s2-s2

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

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title = "Overview of BioCreative II gene mention recognition",

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.",

author = "Larry Smith and Tanabe, {Lorraine K.} and Rie Ando and Kuo, {Cheng Ju} and Chung, {I. Fang} and Hsu, {Chun Nan} and Lin, {Yu Shi} and Roman Klinger and Friedrich, {Christoph M.} and Kuzman Ganchev and Manabu Torii and Hongfang Liu and Barry Haddow and Struble, {Craig A.} and Povinelli, {Richard J.} and Andreas Vlachos and Baumgartner, {William A.} and Lawrence Hunter and Bob Carpenter and Tsai, {Richard Tzong Han} and Dai, {Hong Jie} and Feng Liu and Yifei Chen and Chengjie Sun and Sophia Katrenko and Pieter Adriaans and Christian Blaschke and Rafael Torres and Mariana Neves and Preslav Nakov and Anna Divoli and Manuel Ma{\~n}a-L{\'o}pez and Jacinto Mata and Wilbur, {W. John}",

note = "Funding Information: The work of Rie Johnson was supported by IBM. The work of Roman Klinger and Christoph M Friedrich was funded in part by the Fraunhofer-Max-Planck Cooperation 'Learning and Inference Platform' and the Fraunhofer Society (a public, nonprofit research organization), which also licenses the ProMiner software. The work of Kuzman Ganchev was supported by NSF ITR EIA-0205448. The work of Barry Haddow was funded by ITI Life Sciences, Scotland, whose mission is to explore commercialization of promising technologies in the life sciences. The work of Bob Carpenter was supported by Alias-i and Grant Number R44 RR020259 from the National Center for Research Resources (the content is solely the responsibility of the author and does not necessarily represent the official views of the National Center for Research Resources or the National Institutes of Health). The work of Christian Blaschke and Rafael Torres was supported by Bioalma. The work of Manuel Ma{\~n}a-L{\'o}pez and Jacinto Mata has been partially supported by the Spanish Ministry of Education and Science and the European Union from the European Regional Development Fund (ERDF) - (TIN2005- 08988-C02-02). All other authors have declared that they have no competing interests. Funding Information: This research was supported by the Intramural Research Program of the NIH, NLM, and NCBI.",

year = "2008",

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doi = "10.1186/gb-2008-9-s2-s2",

language = "English (US)",

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journal = "Genome biology",

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T1 - Overview of BioCreative II gene mention recognition

AU - Smith, Larry

AU - Tanabe, Lorraine K.

AU - Ando, Rie

AU - Kuo, Cheng Ju

AU - Chung, I. Fang

AU - Hsu, Chun Nan

AU - Lin, Yu Shi

AU - Klinger, Roman

AU - Friedrich, Christoph M.

AU - Ganchev, Kuzman

AU - Torii, Manabu

AU - Liu, Hongfang

AU - Haddow, Barry

AU - Struble, Craig A.

AU - Povinelli, Richard J.

AU - Vlachos, Andreas

AU - Baumgartner, William A.

AU - Hunter, Lawrence

AU - Carpenter, Bob

AU - Tsai, Richard Tzong Han

AU - Dai, Hong Jie

AU - Liu, Feng

AU - Chen, Yifei

AU - Sun, Chengjie

AU - Katrenko, Sophia

AU - Adriaans, Pieter

AU - Blaschke, Christian

AU - Torres, Rafael

AU - Neves, Mariana

AU - Nakov, Preslav

AU - Divoli, Anna

AU - Maña-López, Manuel

AU - Mata, Jacinto

AU - Wilbur, W. John

N1 - Funding Information: The work of Rie Johnson was supported by IBM. The work of Roman Klinger and Christoph M Friedrich was funded in part by the Fraunhofer-Max-Planck Cooperation 'Learning and Inference Platform' and the Fraunhofer Society (a public, nonprofit research organization), which also licenses the ProMiner software. The work of Kuzman Ganchev was supported by NSF ITR EIA-0205448. The work of Barry Haddow was funded by ITI Life Sciences, Scotland, whose mission is to explore commercialization of promising technologies in the life sciences. The work of Bob Carpenter was supported by Alias-i and Grant Number R44 RR020259 from the National Center for Research Resources (the content is solely the responsibility of the author and does not necessarily represent the official views of the National Center for Research Resources or the National Institutes of Health). The work of Christian Blaschke and Rafael Torres was supported by Bioalma. The work of Manuel Maña-López and Jacinto Mata has been partially supported by the Spanish Ministry of Education and Science and the European Union from the European Regional Development Fund (ERDF) - (TIN2005- 08988-C02-02). All other authors have declared that they have no competing interests. Funding Information: This research was supported by the Intramural Research Program of the NIH, NLM, and NCBI.

PY - 2008/9/1

Y1 - 2008/9/1

N2 - 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.

AB - 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.

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U2 - 10.1186/gb-2008-9-s2-s2

DO - 10.1186/gb-2008-9-s2-s2

M3 - Review article

C2 - 18834493

AN - SCOPUS:51049088874

SN - 1474-7596

VL - 9

JO - Genome biology

JF - Genome biology

IS - SUPPL. 2

M1 - S2

ER -

Overview of BioCreative II gene mention recognition

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