| Sunday, 8 November | Monday, 9 November | Tuesday, 10 November | |
| 8:15 | Registration | ||
| 30 | |||
| 45 | |||
| 9:00 |
Invited talk 1 Thérèse Vachon |
Invited talk 2 Pierre Zweigenbaum |
|
| 15 | |||
| 30 | |||
| 45 | |||
| 10:00 | break | break | |
| 15 | Paper Session 2 | Paper Session 4 | |
| 30 | |||
| 45 | |||
| 11:00 | |||
| 15 | |||
| 30 | |||
| 45 | Best paper award and wrap up | ||
| 12:00 | Registration | Lunch | |
| 15 | Lunch | ||
| 30 | |||
| 45 | |||
| 1:00 |
Tutorial Antonio Jimeno Yepes and Dietrich Rebholz-Schuhmann |
Bus excursion | |
| 15 | Poster spotlight presentations | ||
| 30 | |||
| 45 | Poster session | ||
| 2:00 | |||
| 15 | |||
| 30 | |||
| 45 | break | ||
| 3:00 | Opening remarks | ||
| 15 |
Paper Session 1 | break | |
| 30 |
Paper Session 3 |
||
| 45 | |||
| 4:00 | |||
| 15 | |||
| 30 | |||
| 45 | |||
| 5:00 | |||
| 15 | |||
| 30 | Bus to symposium banquet | ||
| 45 | |||
| 6:00 | |||
| 15 | |||
| 30 | |||
| 45 | |||
| 7:00 | Welcome party | ||
| 15 | |||
| 30 | |||
| 45 | |||
| 8:00 | |||
| 15 | |||
| 30 | |||
| 45 |
| 12:00-1:00 | Registration |
| 1:00-2:45 |
Tutorial Exploitation of Ontological Resources for Information Retrieval and Information Extraction (Antonio Jimeno Yepes and Dietrich Rebholz-Schuhmann) Session Chair: Jong C. Park |
| 2:45-3:00 | Break |
| 3:00-3:15 |
Opening remarks |
|
3:15-5:15 Session 1: Event extraction Session Chair: Dietrich Rebholz-Schuhmann |
|
| 3:15-3:45 |
* Event Extraction with Complex Event Classification using Rich Features (Makoto Miwa, Rune Sætre, Jin-Dong Kim and Junichi Tsujii) |
| 3:45-4:15 |
Biological Event Recognition with Textual Induction (Yutaka Sasaki, Paul Thompson, John McNaught and Sophia Ananiadou) |
| 4:15-4:45 |
Automatic Annotation by BioExcom for categorizing prior and new speculations in biological papers (Julien Desclés, Motasem Alrahabi, Jean-Pierre Desclés and Antoine Blais) |
| 4:45-5:15 |
* Analysis of syntactic and semantic features for fine-grained event-spatial understanding in outbreak news reports (Hutchatai Chanlekha and Nigel Collier) |
| 7:00- | Welcome Party |
| 8:15-9:00 | Registration |
| 9:10-10:00 |
Invited talk 1 Thérèse Vachon Session Chair: Dietrich Rebholz-Schuhmann |
| 10:00-10:15 | Break |
|
10:15-12:15 Session 2: Identifying semantics Session Chair: Nigel Collier |
|
| 10:15-10:45 |
* The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions (Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo and Janet Kelso) |
| 10:45-11:15 |
* The Value of an In-Domain Lexicon in Genomics QA (Yutaka Sasaki, John McNaught and Sophia Ananiadou) |
| 11:15-11:45 |
Automatic Extraction of the Usage Information from the Component Words in Gene Ontology Terms to Enhance Consistency and Predictability (Seung-Cheol Baek and Jong C. Park) |
| 11:45-12:15 |
A Re-evaluation of Biomedical Named Entity - Term Relations (Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim and Jun'ichi Tsujii) |
| 12:15-1:15 | Lunch |
| 1:15-1:45 | Poster spotlight presentations |
| 1:45-3:15 |
Poster session A Thesaurus and an Application Ontology for the Juvenile Arthritis Domain (Ernesto Jim´enez-Ruiz, Rafael Berlanga-Llavori, Victoria Nebot, Antonio Jimeno-Yepes and Dietrich Rebholz-Schuhmann) Comparison of methods for topic template queries in the biomedical domain (Antonio Jimeno-Yepes, Rafael Berlanga-Llavori and, Dietrich Rebholz-Schuhmann) Inference for bio-IE: GENIA meets EKOSS (Jin-Dong Kim, Steven Kraines, Weisen Guo and Jun’ichi Tsujii) ONER: Tool for Organization Named Entity Recognition from Affiliation Strings in PubMed Abstracts (Siddhartha Jonnalagadda, Philip Topham and Graciela Gonzalez) Bio-medical Term Extraction on Simple Rule Language (Takashi Sinnou, Koichi Takeuchi and Nigel Collier) Literature mining for protein acetylation (Youngrae Kim, Hodong Lee and Gwan-Su Yi) Session Chair: Nigel Collier |
| 3:15-3:30 | Break |
|
3:30-5:30 Session 3: Building resources Session Chair: Fabio Rinaldi |
|
| 3:30-4:00 |
Demystifying protein annotations: toward increasing the compatibility of different corpora (Yue Wang, Jin-Dong Kim, Rune Saetre, Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii) |
| 4:00-4:30 |
* The CALBC Silver Standard Corpus - Harmonizing multiple semantic annotations in a large biomedical corpus (Dietrich Rebholz-Schuhmann, Antonio José Jimeno Yepes, Erik M. van Mulligen, Ning Kang, Jan Kors, David Milward, Peter Corbett and Udo Hahn) |
| 4:30-5:00 |
* De-identifying Swedish Clinical Text - Refinement of a Gold Standard and Experiments with Conditional Random Fields (Hercules Dalianis and Sumithra Velupillai) |
| 5:00-5:30 | |
| 5:30- | Bus to symposium banquet |
| 9:10-10:00 |
Invited talk 2 Pierre Zweigenbaum Session Chair: Jong C. Park |
| 10:00-10:15 | Break |
|
10:15-11:45 Session 4: Information extraction Session Chair: See-Kiong Ng |
|
| 10:15-10:45 |
Enabling Recognition of Diseases in Biomedical Text with Machine Learning: Corpus and Benchmark (Robert Leaman, Christopher Miller and Graciela Gonzalez) |
| 10:45-11:15 |
Sentence Simplification Aids Protein-Protein Interaction Extraction (Siddhartha Jonnalagadda and Graciela Gonzalez) |
| 11:15-11:45 |
Effective Mining of Protein Interactions (Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand and Simon Clematide) |
| 11:45-12:00 |
Best paper award and wrap up |
| 12:00-1:00 | Lunch |
| 1:00- | Bus excursion |