| 9:00 | 9:10 | Introduction | |
| 9:10 | 9:30 | Can Literature Analysis Reveal Similarities among Cellular Processes? | M. Chagoyen, P. Carmona-Saez, C. Gil, J.M. Carazo, A. Pascual-Montano |
| 9:30 | 9:50 | The Design of a Wiki-based Curation System for the Ontology of Functions | R. Hoehndorf, K. Prüfer, J. Kelso |
| 9:50 | 10:10 | Distributed Representations of Bio-Ontologies for Semantic Web Services | C.A. Joslyn, D.D.G. Gessler, S.E. Schmidt, K.M. Verspoor |
| 10:10 | 10:30 | SpindleViz: A Three Dimensional, Order Theoretical Visualization Environment for the Gene Ontology | C.A. Joslyn, S.M. Mniszewski, S.A. Smith, P.M. Weber |
| 10:30 | 11:00 | Coffee Break | |
| 11:00 | 12:00 | Invited Speaker | Suzanna Lewis |
| 12:00 | 13:00 | Lunch | |
| 13:00 | 13:20 | Exploring the Construction and Applications of a Protein Description Corpus | M. Krallinger, R. Malik, A. Valencia |
| 13:20 | 13:40 | Improving Biomedical Corpus Annotation Guidelines | Z. Lu, M. Bada, P.V. Ogren, K.B. Cohen, L. Hunter |
| 13:40 | 14:00 | IeXML: Towards a Framework for Interoperability of Text Processing Modules to Improve Annotation of Semantic Types in Biomedical Text | D. Rebholz-Schuhmann, H. Kirsch, G. Nenadic |
| 14:00 | 14:20 | Automatically Adapting an NLP Core Engine to the Biology Domain | E. Buyko, J. Wermter, M. Poprat, U. Hahn |
| 14:20 | 14:30 | 10 Minutes Break | |
| 14:30 | 15:30 | Invited Speaker | Udo Hahn |
| 15:30 | 16:00 | Coffee Break | |
| 16:00 | 16:20 | Improving Biomedical Text Categorisation with NLP | M. Matthews |
| 16:20 | 16:40 | Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence Homology | A. Rechtsteiner, J. Luinstra, C.E..M. Strauss |
| 16:40 | 16:50 | Short Poster Advertisements | |
| 16:50 | 17:50 | Discussion | |
| 17:50 | 18:30 | Poster Session |