[CEUR Workshop Proceedings] 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]


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