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Conference programme

September 1 September 2 September 3
08:15 Registration
08:30 Registration
08:45 Opening remarks
09:00 Tutorial 1
Resources for Semantic Mining: Corpora and Ontologies
Room B2033
Invited talk 1
Alfonso Valencia
Hall Sigma
Invited talk 2
Pierre Zweigenbaum
Hall Lambda
10:00 Break
10:15 Tutorial 1 Break Break
10:30 Session 1
Hall Sigma
Session 4
Hall Delta
11:30 Break
11:45 Tutorial 1 WOPP Session 1
Hall Sigma
WOPP Session 2
Hall Delta
12:15 Lunch Lunch
13:00 Lunch
13:15 Session 2
Hall Sigma
Session 5
Hall Delta
13:45 Tutorial 2
UIMA for Semantic Text Mining
Room B2033
14:30 Break Break
14:45 Break Session 3
Hall Sigma
Poster spotlight presentations
Hall Delta
15:00 Tutorial 2
15:45 Poster session
16:00 Break
16:15 Break Technology spotlight presentation
Hall Sigma
16:30 Tutorial 2
19:00 Welcome reception 20:30 Get-together in the town 17:30 Bus to conference banquet

SMBM'08 program ends on Wednesday, but the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), a related collocated event starting on Wednesday with a shared poster session with SMBM'08, continues yet on Thursday.

Session programme

September 2
Session 1: Information Extraction
10:30-11:45, Hall Sigma
10:30-10:55 Towards Automatic Detection of Experimental Methods from Biomedical Literature
Thomas Kappeler, Simon Clematide, Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi
10:55-11:20 Genic Interaction Extraction by Reasoning on an Ontology
Alain-Pierre Manine, Erick Alphonse and Philippe Bessières
11:20-11:45 Complex-to-Pairwise Mapping of Biological Relationships using a Semantic Network Representation
Juho Heimonen, Sampo Pyysalo, Filip Ginter and Tapio Salakoski
WOPP Session 1
11:45-12:15, Hall Sigma
11:45-12:15 Towards Ontological Interpretations for Improved Text Mining
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Michael Dannemann
Session 2: Tools and Resources
13:15-14:30, Hall Sigma
13:15-13:40 A Tool for the Automatic and Manual Annotation of Biomedical Documents
Anália Lourenço, Sónia Carneiro, Rafael Carreira, Miguel Rocha, Isabel Rocha and Eugénio Ferreira
13:40-14:05 BioLexicon: A Lexical Resource for the Biology Domain
Yutaka Sasaki, Simonetta Montemagni, Piotr Pezik, Dietrich Rebholz-Schuhman, John McNaught and Sophia Ananiadou
14:05-14:30 Exploring the Compatibility of Heterogeneous Protein Annotations Toward Corpus Integration
Yue Wang, Jin-Dong Kim, Rune Sætre and Jun'ichi Tsujii
Session 3: Machine Learning for Information Extraction
14:45-16:00, Hall Sigma
14:45-15:10 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
15:10-15:35 Testing Different ACE-Style Feature Sets for the Extraction of Gene Regulation Relations from MEDLINE Abstracts
Ekaterina Buyko, Elena Beisswanger and Udo Hahn
15:35-16:00 Combining Multiple Layers of Syntactic Information for Protein-Protein Interaction Extraction
Makoto Miwa, Rune Sætre, Yusuke Miyao, Tomoko Ohta and Jun'ichi Tsujii
September 3
Session 4: Ontologies
10:30-11:45, Hall Delta
10:30-10:55 From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Michael Dannemann and Janet Kelso
10:55-11:20 Lexical Properties of OBO Ontology Class Names and Synonyms
Elena Beisswanger, Michael Poprat and Udo Hahn
11:20-11:45 Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary
Hammad Afzal, Robert Stevens and Goran Nenadic
WOPP Session 2
11:45-12:15, Hall Delta
11:45-12:15 Towards Standardisation of Named-Entity Annotations in the Life Science Literature
Dietrich Rebholz-Schuhmann and Goran Nenadic
Session 5: Information Retrieval
13:15-14:30, Hall Delta
13:15-13:40 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
13:40-14:05 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
14:05-14:30 Classifying Disease Outbreak Reports Using N-grams and Semantic Features
Mike Conway, Son Doan, Ai Kawazoe and Nigel Collier
Poster spotlight presentations
14:45-15:45, Hall Delta
Poster session
- How Complex are Complex Protein-protein Interactions?
Jari Björne, Sampo Pyysalo, Filip Ginter and Tapio Salakoski
- Syntactic pattern matching with GraphSpider and MPL
Andrew B. Clegg and Adrian J. Shepherd
- Accurate Conversion of Dependency Parses: Targeting the Stanford Scheme
Katri Haverinen, Filip Ginter, Sampo Pyysalo and Tapio Salakoski
- Classifying Verbs in Biomedical Text Using Subject-Verb-Object Relationships
Pieter van der Horn, Bart Bakker, Gijs Geleijnse, Jan Korst and Sergei Kurkin
- Protein Name Tagging in the Immunological Domain
Renata Kabiljo and Adrian Shepherd
- Towards Knowledge Discovery through Automatic Inference with Text Mining in Biology and Medicine
Hee-Jin Lee and Jong C. Park
- Why Biomedical Relation Extraction Results are Incomparable and What to do about it
Sampo Pyysalo, Rune Sætre, Jun'ichi Tsujii and Tapio Salakoski
- Assessment of Modifying versus Non-modifying Protein Interactions
Dietrich Rebholz-Schuhmann, Antonio Jimeno, Miguel Arregui and Harald Kirsch
- Mining for Gene-Related Key Terms: Where Do We Find Them?
Catalina Tudor, Carl Schmidt and K Vijay-Shanker
- Improving OCR Performance in Biomedical Literature Retrieval through Preprocessing and Postprocessing
Songhua Xu, Jim McCusker, Martin Schultz and Michael Krauthammer

Social Program

A social event is planned for each evening of the three conference days:

Participation in all events is included in SMBM registration and we hope all participants can join us in these events.