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# SMBM 2006
Second International Symposium on Semantic Mining in Biomedicine

### Proceedings of the Second International Symposium on Semantic Mining in Biomedicine
Jena, April 9-12, 2006.

Edited by

### Sophia Ananiadou *
Juliane Fluck #

* National Centre for Text Mining and University of Manchester
# Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)

## Table of Contents

### Papers

1. Automatic Recognition of Topic-Classified Relations between Prostate Cancer and Genes from Medline Abstracts
   (abstract only, see note)
   Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, Jun'ichi Tsujii
2. A critical review of PASBio's argument structures for biomedical verbs
   (abstract only, see note)
   K. Bretonnel Cohen, Lawrence Hunter
3. Three Approaches to GO-Tagging Biomedical Abstracts
   Neil Davis, Henk Harkema, Rob Gaizauskas, Yikun Guo, Moustafa Ghanem, Tom Barnwell, Yike Guo, Jon Ratcliffe:
4. Developing Resources for Swedish Bio-Medical Text Mining
   Dimitrios Kokkinakis
5. Analysing and Classifying Names of Chemical Compounds with CHEMorph
   Gerhard Kremer, Stefanie Anstein, Uwe Reyle
6. Gene Ontology Annotation Using Word Proximity Relationship
   Kevin Hsin-Yih Lin, Wen-Juan Hou, Hsin-Hsi Chen
7. Data Integration through data elements: Mapping data elements to terminological resources
   (abstract only, see note)
   Fleur Mougin, Anita Burgun, Olivier Bodenreider
8. Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches
   (abstract only, see note)
   Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
9. An Environment for Relation Mining over Richly Annotated Corpora: the case of GENIA
   (abstract only, see note)
   Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker
10. Using Dependence Relations in MeSH as a Framework for the Analysis of Disease Information in Medline
    Lowell Vizenor, Olivier Bodenreider

### Posters

1. Biomedical and Chemical Named Entity Recognition with Conditional Random Fields: The Advantage of Dictionary Features
   Christoph M. Friedrich, Thomas Revillion, Martin Hofmann, Juliane Fluck
2. Collecting a Large Corpus from all of Medline
   Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
3. Fitting the finite-state automata platform for mining gene functions from biological scientific literature
   Inès Jilani, Natalia Grabar, Marie-Christine Jaulent
4. Towards a Semantic Description of Bio-Models: Meaning Facets - A Case Study
   Christian Knüpfer, Clemens Beckstein, Peter Dittrich
5. Flexible Text Mining Strategies for Drug Discovery
   David Milward, Christian Blaschke, Jean-Marc Neefs, Mark-Christoph Ott, Rudi Verbeeck, Andrew Stubbs
6. What kind of problems do protein interactions raise for anaphora resolution? - A preliminary analysis
   Olivia Sanchez, Massimo Poesio, Mijail A. Kabadjov, Roman Tesar

Note: Papers marked as 'abstract only' are to appear in BMC Bioinformatics.

submitted by M. Poprat and S. Ananiadou, April 25, 2006