Volume 12 Supplement 8

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


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

The Third BioCreative - Critical Assessment of Information Extraction in Biology Challenge. Go to conference site.

Bethesda, MD, USA

13-15 September 2010

  1. Research

    Overview of the BioCreative III Workshop

    The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological s...

    Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman and Cathy H Wu

    BMC Bioinformatics 2011 12(Suppl 8):S1

    Published on: 3 October 2011

  2. Research

    The gene normalization task in BioCreative III

    We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 full...

    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…

    BMC Bioinformatics 2011 12(Suppl 8):S2

    Published on: 3 October 2011

  3. Research

    The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

    Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional ...

    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…

    BMC Bioinformatics 2011 12(Suppl 8):S3

    Published on: 3 October 2011

  4. Research

    BioCreative III interactive task: an overview

    The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of bi...

    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…

    BMC Bioinformatics 2011 12(Suppl 8):S4

    Published on: 3 October 2011

  5. Research

    Cross-species gene normalization by species inference

    To access and utilize the rich information contained in the biomedical literature, the ability to recognize and normalize gene mentions referenced in the literature is crucial. In this paper, we focus on impro...

    Chih-Hsuan Wei and Hung-Yu Kao

    BMC Bioinformatics 2011 12(Suppl 8):S5

    Published on: 3 October 2011

  6. Research

    Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

    The vast amount of data published in the primary biomedical literature represents a challenge for the automated extraction and codification of individual data elements. Biological databases that rely solely on...

    Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni and Mike Tyers

    BMC Bioinformatics 2011 12(Suppl 8):S8

    Published on: 3 October 2011

  7. Research

    Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions

    Protein-protein interaction (PPI) is an important biomedical phenomenon. Automatically detecting PPI-relevant articles and identifying methods that are used to study PPI are important text mining tasks. In thi...

    Shashank Agarwal, Feifan Liu and Hong Yu

    BMC Bioinformatics 2011 12(Suppl 8):S10

    Published on: 3 October 2011

  8. Research

    Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

    The selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The cont...

    Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz and Sophia Ananiadou

    BMC Bioinformatics 2011 12(Suppl 8):S11

    Published on: 3 October 2011

  9. Research

    A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

    We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we...

    AnĂ¡lia Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay and Luis M Rocha

    BMC Bioinformatics 2011 12(Suppl 8):S12

    Published on: 3 October 2011

    The Erratum to this article has been published in BMC Bioinformatics 2012 13:180