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

BioCreative II.5

Call for papers (News) [2009-10-23]

Special Issue of Transactions in Computational Biology and Bioinformatics

Special Issue on BioCreative II.5

BioCreative (Critical Assessment for Information Extraction in Biology) is the main challenge evaluation in the area of biological text mining, focused on assessment of text mining applied to problems from real biological applications. To date, there have been three BioCreative evaluations; the biological task for the first BioCreative (2003-2004) focused on the automatic extraction and assignment of Gene Ontology (GO) annotations to human proteins based on information from full text articles. The biological task for both BioCreative II (2006-2007) and BioCreative II.5 (2009) focused on the identification of protein-protein interactions, in support for the curation of the IntAct and the MINT protein interaction databases. This series of evaluations has advanced the state of the art in text mining applied to biological problems.

This special issue invites submission of technical papers that describe and analyze the approaches used in the recent BioCreative II.5 evaluation. We encourage papers that describe novel approaches and/or provide analysis of the effectiveness of these approaches in tackling the protein-protein interaction task. In particular, papers must contain novel content not previously published – for guidelines, see here.

Papers will undergo the standard review procedures for TCBB. Authors should indicate their intent to submit a paper by Jan 8, 2010. Please submit your paper to Manuscript Central at by this date. As an author, you are responsible for understanding and adhering to our submission guidelines (available online here). Feel free to contact TCBB’s Publication Coordinator at or the guest editors if you have any questions.

Important Dates

  1. Manuscript Submission Deadline: Friday, Jan. 08, 2010
  2. Initial Decision: Monday, Feb. 15, 2010
  3. Notification of Final Acceptance: Friday, Apr. 30, 2010
  4. Publication Date: July-September 2010

Guest Editors

  • Lynette Hirschman, The MITRE Corporation
  • Martin Krallinger, CNIO
  • Florian Leitner, CNIO
  • Alfonso Valencia, CNIO