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# SMBM 2005
First International Symposium on Semantic Mining in Biomedicine (SMBM)

### First International Symposium on
Semantic Mining in Biomedicine (SMBM)
EBI, Hinxton, UK, 10-12 April 2005.

Edited by

### Udo Hahn *

### Alfonso Valencia **

Organized by

### Dietrich Rebholz-Schuhmann #
Stefan Schulz +

* Computational Linguistics, University of Jena, Germany
* Protein Design Group, Centro Nacional de Biotecnologia, Universidad Autonoma, Madrid, Spain.
# Rebholz Group, European Bioinformatics Institute, Hinxton, UK
+ Medical Informatics, University Hospital, Freiburg, Germany

## Table of Contents

Foreword

1. An ontology of chemical entities helps identify dependence relations among Gene Ontology terms
   Anita Burgun and Olivier Bodenreider, Université de Rennes (F), National Library of Medicine (U.S.A.)
2. Induced Extension of Gene Ontology from Biomedical Resources with Flexible Identification of Candidate Terms (Abstract)
   Jin-Bok Lee, Jung-jae Kim, Jong C. Park KAIST, (South Korea)
3. Automatic Term List Generation for Entity Tagging (Abstract)
   Ted Sandler , Andrew I. Schein and Lyle H. Ungar University of Pennsylvania (U.S.A.)
4. A Relevance Detection Approach to Gene Annotation
   Wen-Juan Hou, Chih Lee, Kevin Hsin-Yih Lin and Hsin-Hsi Chen National Taiwan University (Tw)
5. Recognizing noun phrases in biomedical text: An evaluation of lab prototypes and commercial chunker
   Joachim Wermter, Juliane Fluck, Jannik Stroetgen, Stefan Geißler and Udo Hahn Jena University (D), Fraunhofer Institute SCAI (D), TEMIS Deutschland (D)
6. Tuning text classification for hereditary diseases with section weighting
   Jörg Hakenberg, Juliane Rutsch and Ulf Leser Humboldt-Universität zu Berlin (D), FH Stralsund (D)
7. Combining Light-Weight Retrieval Strategies for Robust Text Categorization (Abstract)
   Patrick Ruch University Hospital of Geneva (Ch)
8. Discovering Paradigm Shift Patterns in Biomedical Abstracts: Application to Neurodegenerative Diseases
   F. Lisacek, C. Chichester, A. Kaplan and A. Sandor Geneva Bioinformatics (Ch), Swiss Institute of Bioinformatics (Ch), Xerox Research Centre Europe (F)
9. Large-scale Extraction of Protein/Gene Relations for Model Organisms (Abstract)
   Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, and Peer Bork EML Research (D), European Molecular Biology Laboratory (D)
10. Protein-Protein Interaction Extraction: A Supervised Learning Approach
    Juan Xiao, Jian Su, GuoDong Zhouand ChewLim Tan Institute for Infocomm Research (Sg), National University of Singapore (Sg)
11. Biomedical Information Extraction with Predicate-Argument Structure Patterns
    Akane Yakushiji, Yusuke Miyao, Yuka Tateisi, Jun’ichi Tsujii University of Tokyo (Jp), CREST, Japan Science and Technology Agency (Jp)

submitted by S. Schulz, August 21, 2005