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List of accepted papers

The following papers have been accepted to be presented at SMBM'08:

Full papers

Authors Title
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Michael Dannemann and Janet Kelso From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories
Sofie Van Landeghem, Yvan Saeys, Bernard De Baets and Yves Van de Peer Extracting protein-protein interactions from text using rich feature vectors and feature selection
Makoto Miwa, Rune Sætre, Yusuke Miyao, Tomoko Ohta and Jun'ichi Tsujii Combining Multiple Layers of Syntactic Information for Protein-Protein Interaction Extraction
Halil Kilicoglu, Marcelo Fiszman, Alejandro Rodriguez, Dongwook Shin, Anna Ripple and Thomas Rindflesch Semantic MEDLINE: A Web Application to Manage the Results of PubMed Searches
Alain-Pierre Manine, Erick Alphonse and Philippe Bessieres Genic interaction extraction by reasoning on an ontology
Filip Ginter, Hanna Suominen, Sampo Pyysalo and Tapio Salakoski Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application
Yue Wang, Jin-Dong Kim, Rune Sætre and Jun'ichi Tsujii Exploring the Compatibility of Heterogeneous Protein Annotations Toward Corpus Integration
Juho Heimonen, Sampo Pyysalo, Filip Ginter and Tapio Salakoski Complex-to-pairwise mapping of biological relationships using a semantic network representation
Anália Lourenço, Sónia Carneiro, Rafael Carreira, Miguel Rocha, Isabel Rocha and Eugénio Ferreira A Tool for the Automatic and Manual Annotation of Biomedical Documents
Mike Conway, Son Doan, Ai Kawazoe and Nigel Collier Classifying Disease Outbreak Reports Using N-grams and Semantic Features
Yutaka Sasaki, Simonetta Montemagni, John McNaught and Sophia Ananiadou A Lexical Resource for the Biology Domain
Hammad Afzal and Goran Nenadic Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary
Ekaterina Buyko, Elena Beisswanger and Udo Hahn Testing Different ACE-Style Feature Sets for the Extraction of Gene Regulation Relations from MEDLINE Abstracts
Elena Beisswanger, Michael Poprat and Udo Hahn Lexical Properties of OBO Ontology Class Names and Synonyms
Thomas Kappeler, Simon Clematide, Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi Towards Automatic Detection of Experimental Methods from Biomedical Literature

Short papers

Katri Haverinen, Filip Ginter, Sampo Pyysalo and Tapio Salakoski Accurate conversion of dependency parses: targeting the Stanford scheme
Pieter van der Horn, Bart Bakker, Gijs Geleijnse, Jan Korst and Sergei Kurkin Classifying verbs in biomedical text using subject-verb-object relationships
Songhua Xu, Jim McCusker, Martin Schultz and Michael Krauthammer Improving OCR Performance in Biomedical Literature Retrieval through Preprocessing and Postprocessing
Andrew B. Clegg and Adrian J. Shepherd Syntactic pattern matching with GraphSpider and MPL
Jari Björne, Sampo Pyysalo, Filip Ginter and Tapio Salakoski How Complex are Complex Protein-protein Interactions?
Renata Kabiljo and Adrian Shepherd Protein name tagging in the immunological domain
Catalina Tudor, Carl Schmidt and Vijay Shanker Mining for gene-related key terms: Where do we find them?
Dietrich Rebholz-Schuhmann, Antonio Jimeno, Miguel Arregui and Harald Kirsch Measuring performance of verbs denoting modifying and non-modifying protein interactions
Sampo Pyysalo, Rune Sætre, Jun'ichi Tsujii and Tapio Salakoski Why Biomedical Relation Extraction Results are Incomparable and What to do about it
Hee-Jin Lee and Jong C. Park Towards Knowledge Discovery through Automatic Inference with Text Mining in Biology and Medicine