Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor 2011-06 Association for Computational Linguistics Portland, Oregon, USA text conference publication ws-2011-bionlp-shared https://aclanthology.org/W11-1800/ Overview of BioNLP Shared Task 2011 Jin-Dong Kim author Sampo Pyysalo author Tomoko Ohta author Robert Bossy author Ngan Nguyen author Jun’ichi Tsujii author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication kim-etal-2011-overview https://aclanthology.org/W11-1801/ 2011-06 1 6 Overview of Genia Event Task in BioNLP Shared Task 2011 Jin-Dong Kim author Yue Wang author Toshihisa Takagi author Akinori Yonezawa author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication kim-etal-2011-overview-genia https://aclanthology.org/W11-1802/ 2011-06 7 15 Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011 Tomoko Ohta author Sampo Pyysalo author Jun’ichi Tsujii author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication ohta-etal-2011-overview https://aclanthology.org/W11-1803/ 2011-06 16 25 Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011 Sampo Pyysalo author Tomoko Ohta author Rafal Rak author Dan Sullivan author Chunhong Mao author Chunxia Wang author Bruno Sobral author Jun’ichi Tsujii author Sophia Ananiadou author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication pyysalo-etal-2011-overview https://aclanthology.org/W11-1804/ 2011-06 26 35 Biomedical Event Extraction from Abstracts and Full Papers using Search-based Structured Prediction Andreas Vlachos author Mark Craven author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication vlachos-craven-2011-biomedical https://aclanthology.org/W11-1805/ 2011-06 36 40 Event Extraction as Dependency Parsing for BioNLP 2011 David McClosky author Mihai Surdeanu author Christopher Manning author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication mcclosky-etal-2011-event-extraction https://aclanthology.org/W11-1806/ 2011-06 41 45 Robust Biomedical Event Extraction with Dual Decomposition and Minimal Domain Adaptation Sebastian Riedel author Andrew McCallum author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication riedel-mccallum-2011-robust https://aclanthology.org/W11-1807/ 2011-06 46 50 Model Combination for Event Extraction in BioNLP 2011 Sebastian Riedel author David McClosky author Mihai Surdeanu author Andrew McCallum author Christopher D Manning author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication riedel-etal-2011-model https://aclanthology.org/W11-1808/ 2011-06 51 55 BioNLP Shared Task 2011 - Bacteria Biotope Robert Bossy author Julien Jourde author Philippe Bessières author Maarten van de Guchte author Claire Nédellec author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication bossy-etal-2011-bionlp https://aclanthology.org/W11-1809/ 2011-06 56 64 BioNLP Shared Task 2011 – Bacteria Gene Interactions and Renaming Julien Jourde author Alain-Pierre Manine author Philippe Veber author Karën Fort author Robert Bossy author Erick Alphonse author Philippe Bessières author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication jourde-etal-2011-bionlp https://aclanthology.org/W11-1810/ 2011-06 65 73 Overview of BioNLP 2011 Protein Coreference Shared Task Ngan Nguyen author Jin-Dong Kim author Jun’ichi Tsujii author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication nguyen-etal-2011-overview https://aclanthology.org/W11-1811/ 2011-06 74 82 Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011 Sampo Pyysalo author Tomoko Ohta author Jun’ichi Tsujii author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication pyysalo-etal-2011-overview-entity https://aclanthology.org/W11-1812/ 2011-06 83 88 The Taming of Reconcile as a Biomedical Coreference Resolver Youngjun Kim author Ellen Riloff author Nathan Gilbert author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication kim-etal-2011-taming https://aclanthology.org/W11-1813/ 2011-06 89 93 Extracting Bacteria Biotopes with Semi-supervised Named Entity Recognition and Coreference Resolution Nhung T H Nguyen author Yoshimasa Tsuruoka author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication nguyen-tsuruoka-2011-extracting https://aclanthology.org/W11-1814/ 2011-06 94 101 BioNLP 2011 Task Bacteria Biotope – The Alvis system Zorana Ratkovic author Wiktoria Golik author Pierre Warnier author Philippe Veber author Claire Nédellec author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication ratkovic-etal-2011-bionlp https://aclanthology.org/W11-1815/ 2011-06 102 111 BioNLP Shared Task 2011: Supporting Resources Pontus Stenetorp author Goran Topić author Sampo Pyysalo author Tomoko Ohta author Jin-Dong Kim author Jun’ichi Tsujii author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication stenetorp-etal-2011-bionlp https://aclanthology.org/W11-1816/ 2011-06 112 120 Sentence Filtering for BioNLP: Searching for Renaming Acts Pierre Warnier author Claire Nédellec author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication warnier-nedellec-2011-sentence https://aclanthology.org/W11-1817/ 2011-06 121 129 Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features Liam R McGrath author Kelly Domico author Courtney D Corley author Bobbie-Jo Webb-Robertson author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication mcgrath-etal-2011-complex https://aclanthology.org/W11-1818/ 2011-06 130 137 Using Kybots for Extracting Events in Biomedical Texts Arantza Casillas author Arantza Díaz de Ilarraza author Koldo Gojenola author Maite Oronoz author German Rigau author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication casillas-etal-2011-using https://aclanthology.org/W11-1819/ 2011-06 138 142 Extracting Biological Events from Text Using Simple Syntactic Patterns Quoc-Chinh Bui author Peter M.A. Sloot author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication bui-sloot-2011-extracting https://aclanthology.org/W11-1820/ 2011-06 143 146 Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction Sofie Van Landeghem author Thomas Abeel author Bernard De Baets author Yves Van de Peer author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication van-landeghem-etal-2011-detecting https://aclanthology.org/W11-1821/ 2011-06 147 148 A Pattern Approach for Biomedical Event Annotation Quang Le Minh author Son Nguyen Truong author Quoc Ho Bao author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication le-minh-etal-2011-pattern https://aclanthology.org/W11-1822/ 2011-06 149 150 An Incremental Model for the Coreference Resolution Task of BioNLP 2011 Don Tuggener author Manfred Klenner author Gerold Schneider author Simon Clematide author Fabio Rinaldi author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication tuggener-etal-2011-incremental https://aclanthology.org/W11-1823/ 2011-06 151 152 Double Layered Learning for Biological Event Extraction from Text Ehsan Emadzadeh author Azadeh Nikfarjam author Graciela Gonzalez author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication emadzadeh-etal-2011-double https://aclanthology.org/W11-1824/ 2011-06 153 154 MSR-NLP Entry in BioNLP Shared Task 2011 Chris Quirk author Pallavi Choudhury author Michael Gamon author Lucy Vanderwende author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication quirk-etal-2011-msr https://aclanthology.org/W11-1825/ 2011-06 155 163 From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text Haibin Liu author Ravikumar Komandur author Karin Verspoor author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication liu-etal-2011-graphs https://aclanthology.org/W11-1826/ 2011-06 164 172 Adapting a General Semantic Interpretation Approach to Biological Event Extraction Halil Kilicoglu author Sabine Bergler author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication kilicoglu-bergler-2011-adapting https://aclanthology.org/W11-1827/ 2011-06 173 182 Generalizing Biomedical Event Extraction Jari Björne author Tapio Salakoski author 2011-06 text Proceedings of BioNLP Shared Task 2011 Workshop Jun’ichi Tsujii editor Jin-Dong Kim editor Sampo Pyysalo editor Association for Computational Linguistics Portland, Oregon, USA conference publication bjorne-salakoski-2011-generalizing https://aclanthology.org/W11-1828/ 2011-06 183 191