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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.


Workshop 1 - BioCreative Workshop on Text Mining Applications [2014-03-26]

Biocuration 2014 Conference at the University of Toronto, Toronto, Canada
Monday April 7, 3-5pm, 2014. East Common Room, Hart House.
Chairs: Cecilia Arighi (1) and Lynette Hirschman (2)
1 Center for Bioinformatics and Computational Biology, University of Delaware, DE, USA
2 The MITRE Corporation, Bedford, MA, USA

BioCreative: Critical Assessment of Information Extraction in Biology is an international community-wide effort that evaluates text mining (TM) and information extraction systems applied to the biomedical domain ( A unique characteristic of this effort is its collaborative and interdisciplinary nature, bringing together experts from various fields, including TM, biocuration, publishing houses and bioinformatics. The aim of this workshop is to demonstrate advances in the application of TM systems, and encourage active involvement of users in guiding TM system development and adoption [1-5].

The topics that will be presented include:
1) The BioCreative Interoperability Initiative: the BioC format has been proposed as a simple extensible mark-up language format to share text documents and annotations. The annotation approach allows the representation of a large number of different annotations to support a variety of applications [6].
2) TM and its users: in this section a brief overview of the BioCreative user interactive task will be presented [7-9] followed by short demos of selected TM systems, a user perspective on current needs and applications of TM tools, and engagement of new communities such as Metagenomics.

Workshop agenda

  • Welcome to workshop, Lynette Hirschman (5 min)
  • Presentations and perspectives, panelists/presenters:
    • a. Interoperability:
      BioC: a minimalist approach to interoperability for biomedical text processing
      Donald Comeau, National Center for Biotechnology Information, National Library of Medicine (15 min)
      b. Text Mining and its users:
      The user interactive task in BioCreative Challenges
      Cecilia Arighi, Center for Bioinformatics and Computational Biology, University of Delaware (15 min)
      BioQRator: a web-based interactive biomedical literature curating system
      Don Comeau, National Center for Biotechnology Information, National Library of Medicine (10 min)
      eCuration: speed curating with PubTator
      Zhiyong Lu, National Center for Biotechnology Information, National Library of Medicine (10 min)
      Semi-automated extraction of experimental methods for assisted curation of RegulonDB
      Fabio Rinaldi, Institute of Computational Linguistics, University of Zurich (10 min)
      The use of text-mining tools during literature triage and functional annotation in the Mouse Genome Database
      Harold Drabkin, MGI, The Jackson Laboratory (10 min)
      Text mining and Publishers
      Bartholomew C Wacek, Elsevier (10 min)
      Reaching out to new user communities: the Metagenomics community
      Lynette Hirschman, The MITRE Corporation (10 min)
  • Open discussion with participants (25 min)
  • BioCreative Organizers: Cecilia N Arighi, Kevin B Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Alfonso Valencia, Thomas C. Wiegers, W John Wilbur, and Cathy H Wu

    1.Hirschman, L., Yeh, A., Blaschke, C. and Valencia, A. (2005) Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics, 6, S1.
    2.Krallinger, M., Morgan, A., Smith, L., Leitner, F., Tanabe, L., Wilbur, J., Hirschman, L. and Valencia, A. (2008) Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biology, 9, S1.
    3.Leitner, F., Mardis, S.A., Krallinger, M., Cesareni, G., Hirschman, L.A. and Valencia, A. (2010) An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform., 7, 385-399.
    4.Arighi, C., Lu, Z., Krallinger, M., Cohen, K., Wilbur, W., Valencia, A., Hirschman, L. and Wu, C. (2011) Overview of the BioCreative III Workshop. BMC Bioinformatics, 12, S1.
    5.BioCreative IV Proceedings:
    6.Comeau D.C., Islamaj Do─čan R., Ciccarese P., Cohen K.B., Krallinger M., Leitner F., Lu Z., Peng Y., Rinaldi F., Torii M., Valencia A., Verspoor K., Wiegers T.C., Wu C.H., Wilbur W.J. BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013 Sep 18;2013:bat064.
    7.Arighi, C., Carterette B., Cohen, K.B., Krallinger, M., Wilbur, W., Fey, P., Dodson, R., Cooper, L., Van Slyke, C.E., Dahdul, W., Mabee, P., et al. (2013) An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. DATABASE, 2013:bas056.
    8.Arighi, C., Roberts, P., Agarwal, S., Bhattacharya, S., Cesareni, G., Chatr-aryamontri, A., Clematide, S., Gaudet, P., Giglio, M., Harrow, I. et al. (2011) BioCreative III interactive task: an overview. BMC Bioinformatics, 12, S4.
    9.Matis Mitchell S., Roberts P., Tudor C.O. and Arighi C.N. BioCreative IV Interactive Task. BioCreative IV Proceedings:Vol 1, pg190 (2013).

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