Appel: BioNLP ST'13, Data Release and 1st Call for Participation

Thierry Hamon thierry.hamon at UNIV-PARIS13.FR
Tue Feb 19 20:23:44 UTC 2013

Date: Tue, 19 Feb 2013 10:37:19 +0100
From: Claire Nedellec <claire.nedellec at>
Message-ID: <512347CF.9000805 at>

(apologies for duplicate posting)
BioNLP Shared Task 2013 -- Training Data Release and First call for

We are pleased to announce the start of the BioNLP Shared Task, the
information extraction task for biology. It is open to any interested

The training and development data sets of BioNLP shared task 2013 are
publicly available on the task Web pages of the BioNLP Shared Task 2013

Supporting resources are available at:

Registration for participation to the BioNLP Shared Task is required.
Registration is open at the BioNLP Shared Task 2013 website:

Please register to list for regular email update by
sending an e-mail to majordomo at with 'subscribe bionlp-st'
in the body of the message. Registered people will be updated with
frequent news about the shared task, e.g. release of supporting tools,
resources, revisions, or other news.

The BioNLP ST workshop will be co-hosted with the ACL/HLT 2013 BioNLP
workshop, to be held in Sofia, Bulgaria, August 8-9 
Participants will be invited to submit manuscripts describing their
systems to the BioNLP ST workshop.


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 are 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)

For further information, please see the shared task website

Training Data Release 12:00 IDLW, 17 Jan. 2013
Test Data Release 22 Mar. 2013
Result Submission 29 Mar. 2013
BioNLP'11 Workshop 8-9 Aug. 2013


Scientific Advisory Board

Jun'ichi Tsujii (Microsoft) - Chair
Philippe Bessières (INRA)
Sung-Pil Choi (KISTI)
Kevin Cohen (Univ. Colorado)
Yuji Kohara (DBCLS)
Tapio Salakoski (Univ. Turku)
Pierre Zweigenbaum (CNRS)

Organizing Committee

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

Programme Committee

Pierre Zweigenbaum, National Center for Scientific Research (CNRS) - PC 

Sophia Ananiadou, University of Manchester (NaCTeM)
Nathalie Aussenac-Gilles, National Center for Scientific Research (CNRS)
Sabine Bergler, Concordia University
Philippe Bessières, National Institute for Agricultural Research (INRA)
Robert Bossy, National Institute for Agricultural Research (INRA)
Kevin Bretonnel Cohen, University of Colorado
Berry de Bruijn, National Research Council (NRC)
Dina Demner-Fushman, National Library of Medicine (NLM)
Jörg Hakenberg, Arizona State University
Jin-Dong Kim, Database Center for Life Science (DBCLS)
Jung-Jae Kim, Nanyang Technological University
Martin Krallinger, National Biotechnology Center (CNB)
David McClosky, Stanford University
Roser Morante, University of Antwerp
Claire Nédellec, National Institute for Agricultural Research (INRA)
Tomoko Ohta, University of Manchester (NaCTeM)
Thierry Poibeau, National Center for Scientific Research (CNRS)
Sampo Pyysalo, University of Manchester (NaCTeM)
Rafal Rak, University of Manchester (NaCTeM)
Sebastian Riedel, University of Massachusetts
Fabio Rinaldi, University of Zurich
Yvan Saeys, Ghent University
Tapio Salakoski, University of Turku
Rune Sætre, Norwegian University of Science and Technology (NTNU)
Özlem Uzuner, State University of New York
Andreas Vlachos (Univ. of Cambridge)

(more members TBA)

    * Web:
    * Mail: bionlp-st-adm at

Mailing list: bionlp-st at
    * for subscription, send an e-mail to majordomo at with 
      "subscribe bionlp-st" in the body of the message.
    * it needs to be a *text* mail.


BioNLP Shared Task 2013 Organizers

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