BioNLP 2009
A workshop of NAACL-HLT 2009
Boulder, Colorado
E-mail: BioNLP2008 arroba googlegroups.com
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Program, talks, and posters

Program - BioNLP 2008


Thursday-Friday, June 4-5, 2009

Day One: listed below

Day Two: see http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/SharedTask/program.shtml

9:00–9:10Opening Remarks
 Session 1: Paper presentations
9:10–9:35Static Relations: a Piece in the Biomedical Information Extraction Puzzle
Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim and Jun’ichi Tsujii
9:35–10:00Distinguishing Historical from Current Problems in Clinical Reports – Which Textual Features Help?
Danielle Mowery, Henk Harkema, John Dowling, Jonathan Lustgarten and Wendy Chapman
10:00–10:25ONYX: A System for the Semantic Analysis of Clinical Text
Lee Christensen, Henk Harkema, Peter Haug, Jeannie Irwin and Wendy Chapman
10:30–11:00morning break
11:00–11:25Learning the Scope of Hedge Cues in Biomedical Texts
Roser Morante and Walter Daelemans
11:25–11:50How 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 and Dietrich Rebholz-Schuhmann
11:50–12:15Extraction of Named Entities from Tables in Gene Mutation Literature
Wern Wong, David Martinez and Lawrence Cavedon
12:15–10:40Selecting an Ontology for Biomedical Text Mining
He Tan and Patrick Lambrix
12:40–2:00lunch break
2:00–2:30Invited speaker: Larry Hunter
2:35–3:00Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon
Rong Xu, Alexander A. Morgan, Amar Das and Alan Garber
3:00–3:25Disambiguation of Biomedical Abbreviations
Mark Stevenson, Yikun Guo, Abdulaziz Alamri and Robert Gaizauskas
3:30–4:00afternoon break
4:00–4:25TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
Thomas Kappeler, Kaarel Kaljurand and Fabio Rinaldi
4:25–4:50Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology
Thierry Hamon and Natalia Grabar
4:50–5:15Towards Automatic Generation of Gene Summary
Feng Jin, Minlie Huang, Zhiyong Lu and Xiaoyan Zhu
 Session 2: Poster presentations
5:00–6:00Incorporating GENETAG-style annotation to GENIA corpus
Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang and Jun’ichi Tsujii
5:00–6:00User-Driven Development of Text Mining Resources for Cancer Risk Assessment
Lin Sun, Anna Korhonen, Ilona Silins and Ulla Stenius
5:00–6:00Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs
Esra Erdem and Reyyan Yeniterzi
5:00–6:00Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports
Vijayaraghavan Bashyam and Ricky K Taira
5:00–6:00Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns
Haibin Liu, Christian Blouin and Vlado Keselj
5:00–6:00Using Hedges to Enhance a Disease Outbreak Report Text Mining System
Mike Conway, Son Doan and Nigel Collier
5:00–6:00Exploring Two Biomedical Text Genres for Disease Recognition
Aurelie Neveol, Won Kim, W. John Wilbur and Zhiyong Lu
5:00–6:00Towards Retrieving Relevant Information for Answering Clinical Comparison Questions
Annette Leonhard
5:00–6:00Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics
Sumire Uematsu, Jin-Dong Kim and Jun’ichi Tsujii
5:00–6:00Evaluation of the Clinical Question Answering Presentation
Yong-Gang Cao, John Ely, Lamont Antieau and Hong Yu
5:00–6:00Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles.
Pawel Matykiewicz, Wlodzislaw Duch and John Pestian
5:00–6:00TEXT2TABLE: Medical Text Summarization System Based on Named Entity Recognition and Modality Identification
Eiji Aramaki, Yasuhide Miura, Masatsugu Tonoike, Tomoko Ohkuma, Hiroshi Mashuichi and Kazuhiko Ohe
5:00–6:00Semantic Annotation of Papers: Interface & Enrichment Tool (SAPIENT)
Maria Liakata, Claire Q and Larisa N. Soldatova




This document last modified 08/09/10 13:08.