Appel: BioNLP Shared Task 2013, 1st announcement, Sample data release

Thierry Hamon thierry.hamon at UNIV-PARIS13.FR
Fri Oct 26 18:19:25 UTC 2012

Date: Wed, 24 Oct 2012 14:10:31 +0200
From: Claire Nedellec <claire.nedellec at>
Message-ID: <5087DAB7.3020403 at>

(apologies for duplicate posting)

BioNLP Shared Task 2013 -- First announcement
Release of sample data sets

We are pleased to announce the upcoming BioNLP Shared Task, an
information extraction task open to any interested participants.  The
task will be held in early 2013, and a workshop on the task is planned
to be co-hosted with the ACL 2013 BioNLP workshop.

Sample data are now available at BioNLP Shared Task 2013 website:

Participation to the task will be open to all interested parties.

The BioNLP Shared Task series represents a community-wide trend in
text-mining for biology toward fine-grained information extraction
(IE). The two previous events, the BioNLP 2009 and 2011 shared task
attracted wide attention, with numerous teams submitting final
results. The task setup and data have since served as the basis of
numerous studies and published event extraction systems and datasets.
The BioNLP Shared Task 2013 (BioNLP-ST'13) follows the general outline
and goals of the previous tasks. It identifies biologically relevant
extraction targets and proposes a linguistically motivated approach to
event representation.  BioNLP-ST'13 tasks also covers many new hot
topics in the biology domain that are close to biologist needs.

As in previous editions, manually annotated data will be provided for
training, development and evaluation of the participating extraction

The six BioNLP-ST 2013 event extraction tasks are

- [GE] Genia Event Extraction for NFkB knowledge base construction
- [CG] Cancer Genetics
- [PC] Pathway Curation
- [GRO] Corpus Annotation with Gene Regulation Ontology
- [RNB] Gene Regulation Network in Bacteria
- [BB] Microorganism biotope (semantic annotation by an ontology)

Tentative schedule is as follows:

      * Sample Data Release    23 October 2013
      * Training Data Release   8 January 2013
      * Test Data Release      March 2013 (Tentative)
      * Result Submission      March 2013 (Tentative)
      * Results Notification   March 2013 (Tentative)
      * Manuscript Submission  April 2013 (Tentative)
      * BioNLP Shared task 2013 workshop   Summer 2013

(subject to extension)

Scientific Advisory Committee
      * Jun'ichi Tsujii (Microsoft) - Chair
      * Sophia Ananiadou (NaCTeM)
      * Kevin Cohen (Univ. Colorado)
      * Sung-Pil Choi (KISTI)
      * Tapio Salakoski (Univ. Turku)
      * Pierre Zweigenbaum (Univ. Paris-Sud, CNRS)

Organizing Committee
      * Claire Nédellec (INRA) - Organizing Chair
      * Robert Bossy (INRA) - Task BB and RBB chair
      * Jin-Dong Kim (DBCLS) - Task GE chair
      * Jung-jae Kim (NTU, Singapore) - Task GRO chair
      * Tomoko Ohta (NaCTeM) - Task PC chair
      * Sampo Pyysalo (NaCTeM) - Task GC chair
      * Julien Jourde (INRA)
      * Pontus Stenetorp (Univ. Tokyo)
      * Yue Wang (DBCLS)

Program Committee
      * TBD

      * Web:
      * Mailing List: bionlp-st at

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