| Vol-714 urn:nbn:de:0074-714-1 Copyright © 2010 for the individual papers by the papers' authors. Copying permitted for private and academic purposes. Re-publication of material from this volume requires permission by the copyright owners. This volume is published by its editors.

# SMBM 2010
International Symposium for Semantic Mining in Biomedicine 2010

### Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine

### Cambridge, United Kingdom, October, 2010.

Edited by

### Nigel Collier 1
Udo Hahn 2
Dietrich Rebholz-Schuhmann 3
Fabio Rinaldi 4
Sampo Pyysalo 5

1 National Institute of Informatics, Japan
2 Jena University, Language & Information Engineering Lab, Germany
3 European Bioinformatics Institute, UK
4 University of Zurich, Switzerland
5 University of Tokyo, Japan

## Table of Contents

### Full papers

1. Automatic Extraction of semantic relations between medical entities: Application to the treatment relation
   Asma Ben Abacha, Pierre Zweigenbaum
2. Towards cross-lingual alerting for bursty epidemic events
   Nigel Collier
3. OMG U got flu? Analysis of shared health messages for bio-surveillance
   Nigel Collier, Son Nguyen Truong, Mai Nguyen Thi Ngoc
4. Applying ontology design patterns to the implementation of relations in GENIA
   Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
5. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference
   Jung-jae Kim, Dietrich Rebholz-Schuhmann
6. Event extraction for DNA methylation
   Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
7. An Analysis of gene/protein associations at PubMed scale
   Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
8. Assessment of NER solutions against the first and second CALBC silver standard corpus
   Dietrich Rebholz-Schuhmann, Antonio Jimeno, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, Rene Witte, Jonas B. Laurila, Christopher JO Baker, Chen-Ju Kuo, Simone Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Furlong, Michael Rautschka, Mariana Lara Neves, Alberto Pascual-Montano, Qi Wei, Nigel Collier, Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik van Mulligen, Jan Kors, Udo Hahn
9. Detecting uncertainty in biomedical literature: a simple disambiguation approach using sparse random indexing
   Erik Velldal
10. Linguistic scope-based and biological event-based speculation and negation annotations in the Genia Event and BioScope corpora
    Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta, Richárd Farkas
11. Coreference based event-argument relation extraction on biomedical text
    Katsumasa Yoshikawa, Sebastian Riedel, Tsutomu Hirao, Masayuki Asahara, Yuji Matsumoto

### Short papers

1. Identifying contextual information in clinical texts: a study of two domains
   Emilia Apostolova, Noriko Tomuro, Dina Demner Fushman
2. Evaluating gene/protein name tagging and mapping for article retrieval
   Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah, Hongfang Liu
3. Biological event extraction using subgraph matching
   Haibin Liu, Vlado Keselj, Christian Blouin
4. Comparing pharmacologic classes in NDF-RT and SNOMED CT
   Jonathan Mortensen, Olivier Bodenreider
5. Species taxonomy for gene name normalization
   György Móra, Richárd Farkas
6. Preventing adverse drug events by extracting information from drug fact sheets
   Stefania Rubrichi, Alex Spengler, Patrick Gallinari, Silvana Quaglini
7. Identification of negated regulation events in the literature: exploring the feature space
   Farzaneh Sarafraz, Goran Nenadic
8. Developing DCO: The DebugIT core ontology for antibiotics resistence modelling
   Daniel Schober, Martin Boeker, Stefan Schulz, Ilinca Tudose
9. A lexical framework for semantic annotation of positive and negative regulation relations in biomedical pathways
   Sine Zambach, Tine Lassen

18-Apr-2011: submitted by Dietrich Rebholz-Schuhmann
18-Apr-2011: published on CEUR-WS.org