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BMC Bioinformatics publishes selected collections of research articles, conference proceedings, reviews and reports as supplements, which are free to access online. All articles published in supplements are subject to peer review; meeting abstracts undergo review and selection by the conference. Find out more about publishing a supplement with BioMed Central.

Volume 12 Supplement 8

The Third BioCreative - Critical Assessment of Information Extraction in Biology Challenge

Research

The Third BioCreative – Critical Assessment of Information Extraction in Biology Challenge

Bethesda, MD, USA

13-15 September 2010

Edited by Cecilia Arighi, Kevin Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Alfonso Valencia, John Wilbur and Cathy Wu

Conference website

Research   Open Access

Overview of the BioCreative III Workshop

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

Abstract | Full text | PDF | PubMed

Research   Open Access

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 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 Wilbur BMC Bioinformatics 2011, 12(Suppl 8):S2 (3 October 2011)

Abstract | Full text | PDF | PubMed

Research   Open Access

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 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)

Abstract | Full text | PDF | PubMed

Research   Open Access

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 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)

Abstract | Full text | PDF | PubMed

Research   Open Access

Cross-species gene normalization by species inference

Chih-Hsuan Wei, Hung-Yu Kao BMC Bioinformatics 2011, 12(Suppl 8):S5 (3 October 2011)

Abstract | Full text | PDF | PubMed

Research   Open Access

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)

Abstract | Full text | PDF | PubMed

Research   Open Access

Multi-stage gene normalization for full-text articles with context-based species filtering for dynamic dictionary entry selection

Richard Tsai, Po-Ting Lai BMC Bioinformatics 2011, 12(Suppl 8):S7 (3 October 2011)

Abstract | Full text | PDF | PubMed

Research   Open Access

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)

Abstract | Full text | PDF | PubMed

Research   Open Access

Classifying protein-protein interaction articles using word and syntactic features

Sun Kim, W Wilbur BMC Bioinformatics 2011, 12(Suppl 8):S9 (3 October 2011)

Abstract | Full text | PDF | PubMed

Research   Open Access

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)

Abstract | Full text | PDF | PubMed

Research   Open Access

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)

Abstract | Full text | PDF | PubMed

Research   Open Access

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)

Abstract | Full text | PDF | PubMed

Research   Open Access

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)

Abstract | Full text | PDF | PubMed


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