This article is part of the supplement: The Third BioCreative – Critical Assessment of Information Extraction in Biology Challenge

Open Access Research

The gene normalization task in BioCreative III

Zhiyong Lu1*, Hung-Yu Kao2, Chih-Hsuan Wei2, Minlie Huang3, Jingchen Liu3, Cheng-Ju Kuo4, Chun-Nan Hsu45, Richard Tzong-Han Tsai6, Hong-Jie Dai78, Naoaki Okazaki9, Han-Cheol Cho10, Martin Gerner11, Illes Solt12, Shashank Agarwal13, Feifan Liu13, Dina Vishnyakova14, Patrick Ruch15, Martin Romacker16, Fabio Rinaldi17, Sanmitra Bhattacharya18, Padmini Srinivasan18, Hongfang Liu19, Manabu Torii20, Sergio Matos21, David Campos21, Karin Verspoor22, Kevin M Livingston22 and W John Wilbur1*

Author Affiliations

1 National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, Maryland 20894, USA

2 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C

3 Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China

4 Institute of Information Science, Academia Sinica, Taipei 115, Taiwan

5 Information Science Institute, University of Southern California, Marina del Rey, California, USA

6 Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C

7 Department of Computer Science, National Tsing-Hua University, Hsinchu, Taiwan, R.O.C

8 Institute of Information Science, Academic Sinica, Taipei, Taiwan, R.O.C

9 Interfaculty Initiative in Information Studies, University of Tokyo, Japan

10 Graduate School of Information Science and Technology, University of Tokyo, Japan

11 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK

12 Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, 1117 Budapest, Hungary

13 Medical Informatics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA

14 BiTem Group, Division of Medical Information Sciences, University of Geneva, Switzerland

15 BiTeM Group, Information Science Department, University of Applied Science, Geneva, Switzerland

16 NITAS/TMS, Text Mining Services, Novartis AG, Switzerland

17 Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland

18 Department of Computer Science, The University of Iowa, Iowa City, Iowa 52242, USA

19 Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905 USA

20 Lab of Text Intelligence in Biomedicine, Georgetown University Medical Center, 4000 Reservoir Rd., NW, Washington, DC 20057 USA

21 DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal

22 Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA

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BMC Bioinformatics 2011, 12(Suppl 8):S2  doi:10.1186/1471-2105-12-S8-S2

Published: 3 October 2011

Additional files

Additional file 1:

GN annotation guidelines (AnnotationGuidelines.pdf)

Format: PDF Size: 62KB Download file

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Open Data

Additional file 2:

Introduction to TAP-k (What is TAP.pdf) The evaluation data and TAP-k software are freely available at the BioCreative III Website: webcite.

Format: PDF Size: 178KB Download file

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Open Data