[Elsnet-list] CALL FOR PARTICIPATION: Second BioCreAtIvE Challenge Evaluation

Martin Krallinger mkrallinger at cnio.es
Tue May 9 17:17:29 CEST 2006

*** Apologies for multiple postings! ***

Second BioCreAtIvE Challenge Evaluation, 2006-2007

We are pleased to announce the second BioCreAtIvE
(Critical Assessment of Information Extraction
systems in Biology) challenge evaluation.

The BioCreAtIvE website can be found at:

If you are interested, please join our mailing list:


BioCreAtIvE is a community-wide effort for evaluating text
mining and information extraction systems applied to the
biological domain. BioCreAtIvE arose out the needs of working
biologists, biological curators and bioinformaticians to access the
wealth of information in the literature, and to link this information to
biological databases and ontologies. BioCreAtIvE focuses on the
comparison of methods and community assessment of scientific
progress, rather than on the purely competitive aspects. The first
BioCreAtIvE challenge evaluation in 2003-2004 attracted broad
interest within the bioinformatics and biomedical text mining community,
with participation from 27 groups from 10 countries. BioCreAtIvE is
organized through collaborations between text mining groups,
biological database curators and bioinformatics researchers.

BioCreAtIvE II Information

BioCreAtIve II will be held during October of 2006, with the workshop
to be held in Spring 2007. It will consist of three tracks. The first
will focus on finding the mentions of genes and proteins in sentences
drawn from MEDLINE abstracts and is the same as Task 1A (Tanabe,
Xie et al. 2005) from BioCreAtIvE I. The second track will involve
producing a list of the EntrezGene identifiers for all the human
genes/proteins mentioned in a collection of MEDLINE abstracts and is
similar to BioCreAtIvE I Task 1B (Hirschman, Colosimo et al. 2005). The
third track of BioCreAtIvE II is new and will involve identifying protein-
protein interactions from full text papers, including extraction of
excerpts from those papers that describe experimentally derived
interactions, for curation into one of two interaction databases:
IntAct (Hermjakob, Montecchi-Palazzi et al. 2004) and MINT
(Zanzoni, Montecchi-Palazzi et al. 2002).

The approximate time line for BioCreAtIvE is as follows:
Jun 2006 Release of training data
Oct 2006 Release and evaluation of test data
Dec 2006 Results returned to participants
Feb 2007 Workshop papers submitted
Mar 2007 Workshop
Jun 2007 Journal articles submitted

We encourage you to visit the web site and sign up
for further information.

Thank you,

Alfonso Valencia
Martin Krallinger
* CNIO - Spanish National Center for Oncology Research

Lynette Hirschman
Alex Morgan
* The MITRE Corporation

W. John Wilbur
Lorrie Tanabe
Larry Smith


Hermjakob, H., L. Montecchi-Palazzi, et al. (2004). "IntAct: an open
source molecular interaction database." Nucleic Acids Res
32(Database issue): D452-5.

Hirschman, L., M. Colosimo, et al. (2005). "Overview of BioCreAtIvE
task 1B: normalized gene lists." BMC Bioinformatics 6 Suppl 1: S11.

Tanabe, L., N. Xie, et al. (2005). "GENETAG: a tagged corpus for
gene/protein named entity recognition." BMC Bioinformatics 6
Suppl 1: S3.

Zanzoni, A., L. Montecchi-Palazzi, et al. (2002). "MINT: a Molecular
INTeraction database." FEBS Lett 513(1): 135-40.

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