Sunday October 24th

14:00 - 17:00 Tutorial

Monday October 25th

09:00 to 09:10 Welcome message and orientation from General Chair(s)

09:10 to 10:10 Invited talk 1: Eric Neumann

Semantic Linked Data in Biomedicine: Shifting the Focus from Application-Centricity to Data-Centricity

10:10 to 10:30 Coffee break

10:30 to 12:00 Oral paper session 1

Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta and Richárd Farkas. Linguistic scope-based and biological event-based speculation and negation annotations in the Genia Event and BioScope corpora

Katsumasa Yoshikawa, Sebastian Riedel, Tsutomu Hirao, Masayuki Asahara and Yuji Matsumoto. Coreference Based Event-Argument Relation Extraction on Biomedical Text

Asma Ben Abacha and Pierre Zweigenbaum. Automatic extraction of semantic relations between medical entities: Application to the treatment relation.

12:00 to 13:30 Lunch

13:30 to 14:30 Invited talk 2: Larry Hunter

Building a Mind for Life

14:30 to 15:30 Coffee break with poster papers

Mary Swift, Nate Blaylock, James Allen, Will de Beaumont, Lucian Galescu and Hyuckchul Jung. Augmenting a deep natural language processing system with UMLS

Jorge Garcia Flores, Mark Deckert, William Turner and Martine Hurault-Plantet. The semantics of involvement: mining the web to locate biomedical expertise

Manabu Torii, Chong Min Lee, Zhang-Zhi Hu and Hongfang Liu. Collecting short-long form pairs from MEDLINE specifically for gene/protein entities

Katalin Lejtovicz and Johann Petrak. Mining Hierarchical Frequent Sequences in Medical Reports for Domain Model Creation

Michael Hughes, Sandeep Modi and Andrew Garrow. Informatics Workflows in the Toxicological Risk Assessment of Food and Cosmetic Ingredients

Vincent Van Asch, Roser Morante and Walter Daelemans. Improving the precision of a relation extraction system by processing negation and speculation

15:30 to 17:30 Oral paper session 2

Nigel Collier. Towards Cross-lingual Alerting for Bursty Epidemic Events

Erik Velldal. Detecting Uncertainty in Biomedical Literature: A Simple Disambiguation Approach Using Sparse Random Indexing

Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii. An Analysis of Gene/Protein Associations at PubMed Scale

Jung-jae Kim and Dietrich Rebholz-Schuhmann. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

Tuesday October 26th

09:00 to 10:00 Invited talk 3: Robert Stevens

The past and future of Knowledge in Biology

10:00 to 10:30 Coffee break

10:30 to 12:00 Oral paper session 3

Nigel Collier, Son Nguyen Truong and Mai Nguyen Thi Ngoc. OMG U got flu? Analysis of shared health messages for bio-surveillance

Tomoko Ohta, Sampo Pyysalo, Makoto Miwa and Jun'ichi Tsujii. Event Extraction for DNA Methylation

Dietrich Rebholz-Schuhmann, Antonio Jimeno, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, Rene Witte, Jonas B. Laurila, Christopher JO Baker, Chen-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Furlong, Michael Rautschka, Mariana Lara Neves, Alberto Pascual-Montano, Qi Wei, Nigel Collier, Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik van Mulligen, Jan Kors and Udo Hahn. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

12:00 to 13:30 Lunch

13:30 to 15:00 Oral paper session 4

Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich and Dietrich Rebholz-Schuhmann. Applying ontology design patterns to the implementation of relations in GENIA

Short papers 5 minutes presentation each

Emilia Apostolova, Noriko Tomuro and Dina Demner Fushman. Identifying Contextual Information in Clinical Texts: A Study of Two Domains

György Móra and Richárd Farkas. Species taxonomy for gene name normalization

Daniel Schober, Martin Boeker, Stefan Schulz and Ilinca Tudose. Developing DCO: The DebugIT Core Ontology for Antibiotics Resistence Modelling

Stefania Rubrichi, Alex Spengler, Patrick Gallinari and Silavana Quaglini. Preventing Adverse Drug Events by Extracting Information from Drug Fact Sheets

Jonathan Mortensen and Olivier Bodenreider. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT

Farzaneh Sarafraz and Goran Nenadic. Identification of Negated Regulation Events in the Literature: Exploring the Feature Space

Sine Zambach and Tine Lassen. A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways

Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah and Hongfang Liu. Evaluating gene/protein name tagging and mapping for article retrieval

Haibin Liu, Vlado Keselj and Christian Blouin. Biological Event Extraction using Subgraph Matching

15:00 to 16:30 Coffee break and short paper poster session

16:30 to 16:45 Best paper award and closing remarks