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Volume 12 Supplement 8

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

Research

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, USA13-15 September 2010

  1. 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...

    Authors: Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman and Cathy H Wu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S1
    Content type: Research Published on:

  2. 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...

    Authors: 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…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S2
    Content type: Research Published on:

  3. 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 ...

    Authors: 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…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S3
    Content type: Research Published on:

  4. 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...

    Authors: 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…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S4
    Content type: Research Published on:

  5. 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...

    Authors: Chih-Hsuan Wei and Hung-Yu Kao
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S5
    Content type: Research Published on:

  6. Previously, gene normalization (GN) systems are mostly focused on disambiguation using contextual information. An effective gene mention tagger is deemed unnecessary because the subsequent steps will filter ou...

    Authors: Cheng-Ju Kuo, Maurice HT Ling and Chun-Nan Hsu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S6
    Content type: Research Published on:

  7. Gene normalization (GN) is the task of identifying the unique database IDs of genes and proteins in literature. The best-known public competition of GN systems is the GN task of the BioCreative challenge, whic...

    Authors: Richard Tzong-Han Tsai and Po-Ting Lai
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S7
    Content type: Research Published on:

  8. 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...

    Authors: Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni and Mike Tyers
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S8
    Content type: Research Published on:

  10. 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...

    Authors: Shashank Agarwal, Feifan Liu and Hong Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S10
    Content type: Research Published on:

  11. 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...

    Authors: Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz and Sophia Ananiadou
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S11
    Content type: Research Published on:

  12. 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...

    Authors: Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay and Luis M Rocha
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S12
    Content type: Research Published on:

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

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