| 9:30-10:00 | Registration |
| 10:00-10:15 | Opening |
| 10:15-12:15 | Session 1[Resource Building] |
|
Integrated Annotation of Biomedical Text: Creating the PennBioIE Corpus
(abstract)
(PDF) Mark Mandel (University of Pennsylvania, USA) GENIA corpus - Linguistic and Semantic Annotation of Biomedical Literature (abstract) (PDF) Jin-dong Kim (GENIA, Univ. of Tokyo, Japan) The Alchemy of Annotation: When Biologists Disagree (abstract) (PDF) Ewan Klein (Edinburgh University, UK) | |
| 12:15-13:30 | Lunch |
| 13:30-15:30 | Session 2 [Computational Biology and Ontology] |
|
An Ontology of Scientific Experiments
(abstract)
(PDF) Ross King (Aberystwyth University, UK) KEGG BRITE: a new addition to KEGG for managing and using functional hierarchies of biological systems (abstract) (PDF) Susumu Goto (Kegg, Kyoto University, Japan) Migrating from the Informal to Formal bio-Ontology: Costs and Benefits (abstract) (PDF) Robert Stevens (Manchester University, UK) | |
| 15:30-16:00 | Break |
| 16:00-18:00 | Session 3[Ontology and Bio-Ontology] |
|
Developing and Using the Gene Ontology
(abstract)
(PDF) Midori Harris (GO Editor, EBI, UK) INOH - pathway data and annotation ontologies (abstract) (PDF) Ken-ichiro Fukuda (AIST, Japan) Ontologies of Time and Events (abstract) (PDF) Jerry Hobbs-ISI (University of Southern California, USA) | |
| 19:00- | Reception |
| 9:00-10:20 | Session 4 [Text Mining and Knowledge Discovery] |
|
Discovery support for life scientists
(abstract)
(QuickTime)
Marc Weeber (University Medical Centre Rotterdam, the Netherlands) Automatic Learning and Populating Ontologies from Web Data (abstract) (PDF) Sergei Sizov (University of Koblenz, Germany) | |
| 10:20-10:40 | Coffee Break |
| 10:40-12:00 | Session 5 [NLP for Scientific Literature] |
|
Deep and shallow processing for e-Chemistry in the SciBorg project
(abstract)
(PDF) Simone Teufel (Cambridge University, UK) Generic NLP technologies and domain adaptation for the analysis of biomedical text (abstract) (PDF) Yusuke Miyao (GENIA, University of Tokyo, Japan) | |
| 12:00-13:15 | Lunch |
| 13:15-15:15 | Session 6 [Service Systems and Practical NLP] |
|
Text Mining support to curation teams: a pipeline of modules for text processing
(abstract)
(PDF) Dietrich Rebholz-Schuhmann (EBI, UK) A Priority Model for Named Entities (abstract) (PDF) John Wilbur (National Library of Medicine, NIH, USA) Building Interaction Networks from MEDLINE with Deep Parsing (abstract) (PDF) Yoshimasa Tsuruoka (GENIA, Univ. of Tokyo, Japan) | |
| 15:15-15:45 | Coffee Break |
| 15:45-17:05 | Session 7[Ontologies, Terminologies and Text Mining] |
|
Text Mining for Knowledge Discovery and Ontology Extension
(abstract)
(PDF) Jong C. Park (KAIST, Korea) Text mining, Ontologies and Natural Language Processing Junichi Tsujii (GENIA, University of Tokyo and NaCTeM, Manchester) | |
| 17:05-17:30 | [Closing Session] |
| Coordinator: Sophia Ananiadou (NaCTeM, University of Manchester) |