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bib (full) Proceedings of the BioNLP 2009 Workshop

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Proceedings of the BioNLP 2009 Workshop
K. Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii | Bonnie Webber

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Static Relations: a Piece in the Biomedical Information Extraction Puzzle
Sampo Pyysalo | Tomoko Ohta | Jin-Dong Kim | Jun’ichi Tsujii

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Distinguishing Historical from Current Problems in Clinical Reports – Which Textual Features Help?
Danielle Mowery | Henk Harkema | John Dowling | Jonathan Lustgarten | Wendy Chapman

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ONYX: A System for the Semantic Analysis of Clinical Text
Lee Christensen | Henk Harkema | Peter Haug | Jeannie Irwin | Wendy Chapman

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Learning the Scope of Hedge Cues in Biomedical Texts
Roser Morante | Walter Daelemans

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How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions
Udo Hahn | Katrin Tomanek | Ekaterina Buyko | Jung-jae Kim | Dietrich Rebholz-Schuhmann

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Extraction of Named Entities from Tables in Gene Mutation Literature
Wern Wong | David Martinez | Lawrence Cavedon

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Selecting an Ontology for Biomedical Text Mining
He Tan | Patrick Lambrix

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Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon
Rong Xu | Alexander A. Morgan | Amar Das | Alan Garber

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Disambiguation of Biomedical Abbreviations
Mark Stevenson | Yikun Guo | Abdulaziz Alamri | Robert Gaizauskas

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TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
Thomas Kappeler | Kaarel Kaljurand | Fabio Rinaldi

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Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology
Thierry Hamon | Natalia Grabar

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Towards Automatic Generation of Gene Summary
Feng Jin | Minlie Huang | Zhiyong Lu | Xiaoyan Zhu

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Incorporating GENETAG-style annotation to GENIA corpus
Tomoko Ohta | Jin-Dong Kim | Sampo Pyysalo | Yue Wang | Jun’ichi Tsujii

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User-Driven Development of Text Mining Resources for Cancer Risk Assessment
Lin Sun | Anna Korhonen | Ilona Silins | Ulla Stenius

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Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs
Esra Erdem | Reyyan Yeniterzi

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Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports
Vijayaraghavan Bashyam | Ricky K Taira

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Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns
Haibin Liu | Christian Blouin | Vlado Kešelj

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Using Hedges to Enhance a Disease Outbreak Report Text Mining System
Mike Conway | Son Doan | Nigel Collier

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Exploring Two Biomedical Text Genres for Disease Recognition
Aurélie Névéol | Won Kim | W. John Wilbur | Zhiyong Lu

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Towards Retrieving Relevant Information for Answering Clinical Comparison Questions
Annette Leonhard

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Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics
Sumire Uematsu | Jin-Dong Kim | Jun’ichi Tsujii

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Evaluation of the Clinical Question Answering Presentation
Yong-Gang Cao | John Ely | Lamont Antieau | Hong Yu

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Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles.
Pawel Matykiewicz | Wlodzislaw Duch | John Pestian

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TEXT2TABLE: Medical Text Summarization System Based on Named Entity Recognition and Modality Identification
Eiji Aramaki | Yasuhide Miura | Masatsugu Tonoike | Tomoko Ohkuma | Hiroshi Mashuichi | Kazuhiko Ohe

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Semantic Annotation of Papers: Interface & Enrichment Tool (SAPIENT)
Maria Liakata | Claire Q | Larisa N. Soldatova

pdf (full)
bib (full) Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task

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Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task
Jun’ichi Tsujii

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Overview of BioNLP’09 Shared Task on Event Extraction
Jin-Dong Kim | Tomoko Ohta | Sampo Pyysalo | Yoshinobu Kano | Jun’ichi Tsujii

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Extracting Complex Biological Events with Rich Graph-Based Feature Sets
Jari Björne | Juho Heimonen | Filip Ginter | Antti Airola | Tapio Pahikkala | Tapio Salakoski

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Event Extraction from Trimmed Dependency Graphs
Ekaterina Buyko | Erik Faessler | Joachim Wermter | Udo Hahn

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UZurich in the BioNLP 2009 Shared Task
Kaarel Kaljurand | Gerold Schneider | Fabio Rinaldi

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Biomedical Event Extraction without Training Data
Andreas Vlachos | Paula Buttery | Diarmuid Ó Séaghdha | Ted Briscoe

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A Markov Logic Approach to Bio-Molecular Event Extraction
Sebastian Riedel | Hong-Woo Chun | Toshihisa Takagi | Jun’ichi Tsujii

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High-precision biological event extraction with a concept recognizer
K. Bretonnel Cohen | Karin Verspoor | Helen Johnson | Chris Roeder | Philip Ogren | William Baumgartner | Elizabeth White | Lawrence Hunter

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A memory-based learning approach to event extraction in biomedical texts
Roser Morante | Vincent Van Asch | Walter Daelemans

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Extraction of biomedical events using case-based reasoning
Mariana Neves | José-María Carazo | Alberto Pascual-Montano

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Biomedical Event Annotation with CRFs and Precision Grammars
Andrew MacKinlay | David Martinez | Timothy Baldwin

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Molecular event extraction from Link Grammar parse trees
Jörg Hakenberg | Illés Solt | Domonkos Tikk | Luis Tari | Astrid Rheinländer | Nguyen Quang Long | Graciela Gonzalez | Ulf Leser

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Tunable Domain-Independent Event Extraction in the MIRA Framework
Georgi Georgiev | Kuzman Ganchev | Vassil Momchev | Deyan Peychev | Preslav Nakov | Angus Roberts

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BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing
Syed Toufeeq Ahmed | Radhika Nair | Chintan Patel | Hasan Davulcu

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From Protein-Protein Interaction to Molecular Event Extraction
Rune Sætre | Makoto Miwa | Kazuhiro Yoshida | Jun’ichi Tsujii

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A Multi-Phase Approach to Biomedical Event Extraction
Hyoung-Gyu Lee | Han-Cheol Cho | Min-Jeong Kim | Joo-Young Lee | Gumwon Hong | Hae-Chang Rim

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Supervised Classification for Extracting Biomedical Events
Arzucan Özgür | Dragomir Radev

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Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances
Farzaneh Sarafraz | James Eales | Reza Mohammadi | Jonathan Dickerson | David Robertson | Goran Nenadic

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Syntactic Dependency Based Heuristics for Biological Event Extraction
Halil Kilicoglu | Sabine Bergler

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Analyzing text in search of bio-molecular events: a high-precision machine learning framework
Sofie Van Landeghem | Yvan Saeys | Bernard De Baets | Yves Van de Peer

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Exploring ways beyond the simple supervised learning approach for biological event extraction
György Móra | Richárd Farkas | György Szarvas | Zsolt Molnár