NaCTeM

Special issue of BMC Bioinformatics on BioCreative III

2011-11-23

NaCTeM's participation in BioCreative III is reported in an article within a special issue of BMC Bioinformatics, which is now available on line at:

http://www.biomedcentral.com/bmcbioinformatics/12?issue=S8

Table of Contents

Research
Overview of the BioCreative III Workshop
Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H Wu
BMC Bioinformatics 2011, 12(Suppl 8):S1 (3 October 2011)

Research
The gene normalization task in BioCreative III
Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sergio Matos, David Campos, Karin Verspoor, Kevin M Livingston, W John Wilbur
BMC Bioinformatics 2011, 12(Suppl 8):S2 (3 October 2011)

Research
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W John Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu, et al.
BMC Bioinformatics 2011, 12(Suppl 8):S3 (3 October 2011)

Research
BioCreative III interactive task: an overview
Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Gwinn Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E Thomas, Luca Toldo, Lynette Hirschman, Cathy H Wu
BMC Bioinformatics 2011, 12(Suppl 8):S4 (3 October 2011)

Research
Cross-species gene normalization by species inference
Chih-Hsuan Wei, Hung-Yu Kao
BMC Bioinformatics 2011, 12(Suppl 8):S5 (3 October 2011)

Research
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization
Cheng-Ju Kuo, Maurice HT Ling, Chun-Nan Hsu
BMC Bioinformatics 2011, 12(Suppl 8):S6 (3 October 2011)

Research
Multi-stage gene normalization for full-text articles with context-based species filtering for dynamic dictionary entry selection
Richard Tzong-Han Tsai, Po-Ting Lai
BMC Bioinformatics 2011, 12(Suppl 8):S7 (3 October 2011)

Research
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases
Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers
BMC Bioinformatics 2011, 12(Suppl 8):S8 (3 October 2011)

Research
Classifying protein-protein interaction articles using word and syntactic features
Sun Kim, W John Wilbur
BMC Bioinformatics 2011, 12(Suppl 8):S9 (3 October 2011)

Research
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions
Shashank Agarwal, Feifan Liu, Hong Yu
BMC Bioinformatics 2011, 12(Suppl 8):S10 (3 October 2011)

Research
Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature
Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz, Sophia Ananiadou
BMC Bioinformatics 2011, 12(Suppl 8):S11 (3 October 2011)

Research
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature
Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M Rocha
BMC Bioinformatics 2011, 12(Suppl 8):S12 (3 October 2011)

Research
Detection of interaction articles and experimental methods in biomedical literature
Gerold Schneider, Simon Clematide, Fabio Rinaldi
BMC Bioinformatics 2011, 12(Suppl 8):S13 (3 October 2011)

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