Volume 13 Supplement 11

Selected articles from the BioNLP Shared Task 2011


Edited by Jin-Dong Kim, Sampo Pyysalo, Claire Nédellec, Sophia Ananiadou and Jun'ichi Tsujii

BioNLP Shared Task 2011. Go to conference site.

Portland, OR, USA

23-24 June 2011

  1. Proceedings

    The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011

    The Genia task, when it was introduced in 2009, was the first community-wide effort to address a fine-grained, structural information extraction from biomedical literature. Arranged for the second time as one ...

    Jin-Dong Kim, Ngan Nguyen, Yue Wang, Jun'ichi Tsujii, Toshihisa Takagi and Akinori Yonezawa

    BMC Bioinformatics 2012 13(Suppl 11):S1

    Published on: 26 June 2012

  2. Proceedings

    Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

    We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI),...

    Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun'ichi Tsujii and Sophia Ananiadou

    BMC Bioinformatics 2012 13(Suppl 11):S2

    Published on: 26 June 2012

  3. Proceedings

    BioNLP Shared Task - The Bacteria Track

    We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. Th...

    Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte, Philippe Bessières and Claire Nédellec

    BMC Bioinformatics 2012 13(Suppl 11):S3

    Published on: 26 June 2012

  4. Proceedings

    University of Turku in the BioNLP'11 Shared Task

    We present a system for extracting biomedical events (detailed descriptions of biomolecular interactions) from research articles, developed for the BioNLP'11 Shared Task. Our goal is to develop a system easily...

    Jari Björne, Filip Ginter and Tapio Salakoski

    BMC Bioinformatics 2012 13(Suppl 11):S4

    Published on: 26 June 2012

  5. Proceedings

    Semantically linking molecular entities in literature through entity relationships

    Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of det...

    Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski and Yves Van de Peer

    BMC Bioinformatics 2012 13(Suppl 11):S6

    Published on: 26 June 2012

  6. Proceedings

    Biological event composition

    In recent years, biological event extraction has emerged as a key natural language processing task, aiming to address the information overload problem in accessing the molecular biology literature. The BioNLP ...

    Halil Kilicoglu and Sabine Bergler

    BMC Bioinformatics 2012 13(Suppl 11):S7

    Published on: 26 June 2012

  7. Proceedings

    Combining joint models for biomedical event extraction

    We explore techniques for performing model combination between the UMass and Stanford biomedical event extraction systems. Both sub-components address event extraction as a structured prediction problem, and u...

    David McClosky, Sebastian Riedel, Mihai Surdeanu, Andrew McCallum and Christopher D Manning

    BMC Bioinformatics 2012 13(Suppl 11):S9

    Published on: 26 June 2012