Appel: BioNLP Main Shared Task (BioNLP-ST'2011)

Thierry Hamon thierry.hamon at UNIV-PARIS13.FR
Sat Jan 15 20:53:02 UTC 2011

Date: Fri, 14 Jan 2011 10:15:32 +0100
From: Claire Nedellec <claire.nedellec at>
Message-ID: <4D301434.6000902 at>

(apologies for duplicate posting)

We are pleased to announce the BioNLP Shared Task 2011.

The BioNLP Shared Task series represents a community-wide trend in
bio-textmining toward fine-grained information extraction (IE). The
first event, the BioNLP 2009 shared task (Dec. 2008-March 2009),
attracted wide attention, with 24 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 2011 (BioNLP-ST'11) is the follow-up event to
the BioNLP 2009 shared task. While following the general outline and
goals of the previous task in defining biologically relevant
extraction targets and a linguistically motivated approach to event
representation, the tasks generalize and extend on the previous in
three key aspects: text type, domain, and targeted event
types. Manually annotated data where all the annotations are bound to
specific expressions in the text are provided for training,
development and evaluation of extraction methods, and tools for
detailed evaluation of system outputs are available. Participation to
the task is open to all interested parties.

The participation to the supporting tasks is now closed (14 Sept to 31
Oct. 2010).
The Main tasks are currently running. (1Dec 2010 to 8 March 2011)

The five BioNLP-ST 2011 event extraction tasks are
- [EPI] Epigenetics and Post-translational Modifications
- [ID] Infectious Diseases
- Bacteria Track:
       + [BB] Biotopes
       + [BI] Genic interactions

For details on the shared task, please see the shared task website


Main Tasks
     Training Data Release  1 Dec. 2010
     Test Data Release      1 Mar. 2011
     Result Submission      8 Mar. 2011
     Results Notification  10 Mar. 2011
Manuscript Submission       8 Apr. 2011


Scientific Advisory Committee
     * Jun'ichi Tsujii (Univ. Tokyo, NaCTeM) - Chair
     * Sophia Ananiadou (NaCTeM, Manchester)
     * Kevin Cohen (MITRE)
     * Claire Nedellec (INRA)
     * Andrey Rzhetsky (Univ. Chicago)
     * Bruno Sobral (Virginia Bioinformatics Inst.)
     * Tapio Salakoski (Univ. Turku)
     * Toshihisa Takagi (DBCLS)

Organizing Committee
     * Jin-Dong Kim (DBCLS) - Chair
     * Sampo Pyysalo (Univ. Tokyo) - Chair
     * Tomoko Ohta (Univ. Tokyo)
     * Robert Bossy (INRA)
     * Chunhong Mao (Virginia Bioinformatics Inst.)
     * Dan Sullivan (Virginia Bioinformatics Inst.)
     * Rafal Rak (NaCTeM, Manchester)
     * Nguyen Luu Thuy Ngan (Univ. Tokyo)

     * Web:
     * Mail: bionlp-st at

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