[Elsnet-list] BioNLP ST'13: Data Release and 1st Call for Participation

Sampo Pyysalo sampo.pyysalo at gmail.com
Fri Jan 18 10:13:04 CET 2013

(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

We are beginning the release of training and development data sets of
BioNLP shared task 2013. They are publicly available on the task Web pages
of the BioNLP Shared Task 2013 website:
http://2013.bionlp-st.org/**tasks <http://2013.bionlp-st.org/tasks>

Release of data sets for some tasks are being delayed, but should be
completed within a couple of days, which will be notified to the
registered people.
Supporting resources will be released in a couple of days.

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

Please register to bionlp-st.org list for regular email update by sending
an e-mail to majordomo at bionlp-st.org 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 methods.

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)
Sabine Bergler, Concordia University
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)
Roser Morante, University of Antwerp
Claire Nédellec, National Institute for Agricultural Research (INRA)
Tomoko Ohta, University of Manchester (NaCTeM)
Sampo Pyysalo, University of Manchester (NaCTeM)
Rafal Rak, University of Manchester (NaCTeM)
Yvan Saeys, Ghent University
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: http://2013.bionlp-st.org/
   * Mail: bionlp-st-adm at googlegroups.com

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

   * https://sites.google.com/site/**bionlpst2013/registration<https://sites.google.com/site/bionlpst2013/registration>

BioNLP Shared Task 2013 Organizers
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