Workshop Programme

Time Presentation
09:15-09:30 Welcome, by Sophia Ananiadou
09:30-10:30 Invited talk, chaired by Kevin Cohen
09:30-10:30 Jun'ichi Tsujii, Microsoft Research Asia
Semantic and linguistic annotations in GENIA
10:30-11:00 Coffee Break
11:00-12:15 Session 1, chaired by Paul Thompson
11:00-11:25 Claudiu Mihăilă, Riza Theresa Batista-Navarro, Sophia Ananiadou
Analysing Entity Type Variation across Biomedical Subdomains
Paper
11:25-11:50 Suwisa Kaewphan, Sanna Kreula, Sofie Van Landeghem, Yves Van de Peer, Patrik R. Jones and Filip Ginter
Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP(H) Metabolism in E. coli with Event Extraction
Paper
11:50-12:15 Mariana Neves, Alexander Damaschun, Andreas Kurtz and Ulf Leser
Annotating and Evaluating Text for Stem Cell Research
Paper Presentation
12:45-14:00 Lunch break
14:00-14:15 Session 2, chaired by Kevin Cohen
14:00-14:25 Raheel Nawaz, Paul Thompson and Sophia Ananiadou
Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers
Paper Presentation
14:25-14:50 Fei Xia and Meliha Yetisgen-Yildiz
Clinical Corpus Annotation: Challenges and Strategies
Paper Presentation
14:50-15:15 Dimitrios Kokkinakis
The Journal of the Swedish Medical Association - a Corpus Resource for Biomedical Text Mining in Swedish
Paper Presentation
15:15-15:45 Session 3, chaired by Paul Thompson
15:15-15:25 Hercules Dalianis and Henrik Boström
Releasing a Swedish Clinical Corpus after Removing All Words - De-Identification Experiments with Conditional Random Fields and Random Forests
Paper Presentation
15:25-15:35 Alyaa Alfalahi, Sara Brissman and Hercules Dalianis
Pseudonymisation of Personal Names and other PHIs in an Annotated Clinical Swedish Corpus
Paper Presentation
15:35-15:45 Olfa Makkaoui, Julien Desclés and Jean-Pierre Desclés
Evaluation and Performance Improvement of the BioExcom System for the Automatic Detection of Speculation in Biomedical Texts
Paper Presentation
15:45-16:30 Poster session and coffee break
16:30-17:20 Session 4, chaired by Sophia Ananiadou
16:30-16:55 Philippe Thomas, Tamara Bobić, Martin Hofmann-Apitius, Ulf Leser and Roman Klinger
Weakly Labeled Corpora as Silver Standard for Drug-Drug and Protein-Protein Interaction
Paper
16:55-17:20 Amber Stubbs
Developing Specifications for Light Annotation Tasks in the Biomedical Domain
Paper Presentation
17:20-17:30 Concluding remarks, by Sophia Ananiadou