Thursday, June 4, 2009 |
| 9:00–9:10 | Opening Remarks |
| | Session 1: Paper presentations |
| 9:10–9:35 | Static Relations: a Piece in the Biomedical Information Extraction Puzzle
Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim and Jun’ichi Tsujii |
| 9:35–10:00 | Distinguishing Historical from Current Problems in Clinical Reports – Which Textual Features Help?
Danielle Mowery, Henk Harkema, John Dowling, Jonathan Lustgarten and Wendy Chapman |
| 10:00–10:25 | ONYX: A System for the Semantic Analysis of Clinical Text
Lee Christensen, Henk Harkema, Peter Haug, Jeannie Irwin and Wendy Chapman |
| 10:30–11:00 | morning break |
| 11:00–11:25 | Learning the Scope of Hedge Cues in Biomedical Texts
Roser Morante and Walter Daelemans |
| 11:25–11:50 | 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 and Dietrich Rebholz-Schuhmann |
| 11:50–12:15 | Extraction of Named Entities from Tables in Gene Mutation Literature
Wern Wong, David Martinez and Lawrence Cavedon |
| 12:15–10:40 | Selecting an Ontology for Biomedical Text Mining
He Tan and Patrick Lambrix |
| 12:40–2:00 | lunch break |
| 2:00–2:30 | Invited Talk |
| 2:35–3:00 | Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon
Rong Xu, Alexander A. Morgan, Amar Das and Alan Garber |
| 3:00–3:25 | Disambiguation of Biomedical Abbreviations
Mark Stevenson, Yikun Guo, Abdulaziz Alamri and Robert Gaizauskas |
| 3:30–4:00 | afternoon break |
| 4:00–4:25 | TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
Thomas Kappeler, Kaarel Kaljurand and Fabio Rinaldi |
| 4:25–4:50 | Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology
Thierry Hamon and Natalia Grabar |
| 4:50–5:15 | Towards Automatic Generation of Gene Summary
Feng Jin, Minlie Huang, Zhiyong Lu and Xiaoyan Zhu |
| | Session 2: Poster presentations |
| 5:00–6:00 | Incorporating GENETAG-style annotation to GENIA corpus
Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang and Jun’ichi Tsujii |
| 5:00–6:00 | User-Driven Development of Text Mining Resources for Cancer Risk Assessment
Lin Sun, Anna Korhonen, Ilona Silins and Ulla Stenius |
| 5:00–6:00 | Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs
Esra Erdem and Reyyan Yeniterzi |
| 5:00–6:00 | Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports
Vijayaraghavan Bashyam and Ricky K Taira |
| 5:00–6:00 | Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns
Haibin Liu, Christian Blouin and Vlado Keselj |
| 5:00–6:00 | Using Hedges to Enhance a Disease Outbreak Report Text Mining System
Mike Conway, Son Doan and Nigel Collier |
| 5:00–6:00 | Exploring Two Biomedical Text Genres for Disease Recognition
Aurelie Neveol, Won Kim, W. John Wilbur and Zhiyong Lu |
| 5:00–6:00 | Towards Retrieving Relevant Information for Answering Clinical Comparison Questions
Annette Leonhard |
| 5:00–6:00 | Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics
Sumire Uematsu, Jin-Dong Kim and Jun’ichi Tsujii |
| 5:00–6:00 | Evaluation of the Clinical Question Answering Presentation
Yong-Gang Cao, John Ely, Lamont Antieau and Hong Yu |
| 5:00–6:00 | Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles.
Pawel Matykiewicz, Wlodzislaw Duch and John Pestian |
| 5:00–6:00 | TEXT2TABLE: 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 |
| 5:00–6:00 | Semantic Annotation of Papers: Interface & Enrichment Tool (SAPIENT)
Maria Liakata, Claire Q and Larisa N. Soldatova |