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Proceedings

  • The full proceedings as printed for SMBM'08 can be downloaded here.
  • BibTeX file for the SMBM proceedings can be downloaded here

The individual papers as they appeared in the printed proceedings are downloadable below:

1 Text Mining Methods as Computational Biology Tools
Alfonso Valencia
3-4 Natural Language Processing in the Medical and Biological Domains: a Parallel Perspective
Pierre Zweigenbaum
5-12 Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary
Hammad Afzal, Robert Stevens and Goran Nenadic
13-20 Lexical Properties of OBO Ontology Class Names and Synonyms
Elena Beisswanger, Michael Poprat and Udo Hahn
21-28 Testing Different ACE-Style Feature Sets for the Extraction of Gene Regulation Relations from MEDLINE Abstracts
Ekaterina Buyko, Elena Beisswanger and Udo Hahn
29-36 Classifying Disease Outbreak Reports Using N-grams and Semantic Features
Mike Conway, Son Doan, Ai Kawazoe and Nigel Collier
37-44 Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application
Filip Ginter, Hanna Suominen, Sampo Pyysalo and Tapio Salakoski
45-52 Complex-to-Pairwise Mapping of Biological Relationships using a Semantic Network Representation
Juho Heimonen, Sampo Pyysalo, Filip Ginter and Tapio Salakoski
53-60 From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Michael Dannemann and Janet Kelso
61-68 Towards Automatic Detection of Experimental Methods from Biomedical Literature
Thomas Kappeler, Simon Clematide, Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi
69-76 Semantic MEDLINE: A Web Application to Manage the Results of PubMed Searches
Halil Kilicoglu, Marcelo Fiszman, Alejandro Rodriguez, Dongwook Shin, Anna Ripple and Thomas Rindflesch
77-84 Extracting Protein-Protein Interactions from Text using Rich Feature Vectors and Feature Selection
Sofie Van Landeghem, Yvan Saeys, Bernard De Baets and Yves Van de Peer
85-92 A Tool for the Automatic and Manual Annotation of Biomedical Documents
Anália Lourenço, Sónia Carneiro, Rafael Carreira, Miguel Rocha, Isabel Rocha and Eugénio Ferreira
93-100 Genic Interaction Extraction by Reasoning on an Ontology
Alain-Pierre Manine, Erick Alphonse and Philippe Bessières
101-108 Combining Multiple Layers of Syntactic Information for Protein-Protein Interaction Extraction
Makoto Miwa, Rune Sætre, Yusuke Miyao, Tomoko Ohta and Jun'ichi Tsujii
109-116 BioLexicon: A Lexical Resource for the Biology Domain
Yutaka Sasaki, Simonetta Montemagni, Piotr Pezik, Dietrich Rebholz-Schuhman, John McNaught and Sophia Ananiadou
117-124 Exploring the Compatibility of Heterogeneous Protein Annotations Toward Corpus Integration
Yue Wang, Jin-Dong Kim, Rune Sætre and Jun'ichi Tsujii
125-128 How Complex are Complex Protein-protein Interactions?
Jari Björne, Sampo Pyysalo, Filip Ginter and Tapio Salakoski
129-132 Syntactic pattern matching with GraphSpider and MPL
Andrew B. Clegg and Adrian J. Shepherd
133-136 Accurate Conversion of Dependency Parses: Targeting the Stanford Scheme
Katri Haverinen, Filip Ginter, Sampo Pyysalo and Tapio Salakoski
137-140 Classifying Verbs in Biomedical Text Using Subject-Verb-Object Relationships
Pieter van der Horn, Bart Bakker, Gijs Geleijnse, Jan Korst and Sergei Kurkin
141-144 Protein Name Tagging in the Immunological Domain
Renata Kabiljo and Adrian Shepherd
145-148 Towards Knowledge Discovery through Automatic Inference with Text Mining in Biology and Medicine
Hee-Jin Lee and Jong C. Park
149-152 Why Biomedical Relation Extraction Results are Incomparable and What to do about it
Sampo Pyysalo, Rune Sætre, Jun'ichi Tsujii and Tapio Salakoski
153-156 Assessment of Modifying versus Non-modifying Protein Interactions
Dietrich Rebholz-Schuhmann, Antonio Jimeno, Miguel Arregui and Harald Kirsch
157-160 Mining for Gene-Related Key Terms: Where Do We Find Them?
Catalina Tudor, Carl Schmidt and K Vijay-Shanker
161-164 Improving OCR Performance in Biomedical Literature Retrieval through Preprocessing and Postprocessing
Songhua Xu, Jim McCusker, Martin Schultz and Michael Krauthammer
165-166 Towards Ontological Interpretations for Improved Text Mining
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Michael Dannemann
167-169 Towards Standardisation of Named-Entity Annotations in the Life Science Literature
Dietrich Rebholz-Schuhmann and Goran Nenadic