Proceedings
- Proceedings: Entire volume, Front Matter
BioNLP-ST Workshop (Friday, August 9, 2013)
| (8:30-9:00) Welcome and Introduction | ||
| 08:45 | Overview of BioNLP Shared Task 2013 Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo and Pierre Zweigenbaum | |
| Session 1: (9:00-10:30) Oral Presentations: Genia Event Extraction and Gene Regulation Ontology | ||
| 9:00 | The Genia Event Extraction Shared Task, 2013 Edition - Overview Jin-Dong Kim, Yue Wang and Yamamoto Yasunori | |
| 9:10–9:30 | TEES 2.1: Automated Annotation Scheme Learning in the BioNLP 2013 Shared Task Jari Björne and Tapio Salakoski | |
| 9:30–9:50 | EVEX in ST’13: Application of a large-scale text mining resource to event extraction and network construction Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer and Filip Ginter | |
| 9:50–10:10 | Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data Andrew MacKinlay, David Martinez, Antonio Jimeno Yepes, Haibin Liu, W John Wilbur and Karin Verspoor | |
| 10:10–10:30 | Biomedical Event Extraction by Multi-class Classification of Pairs of Text Entities Xiao Liu, Antoine Bordes and Yves Grandvalet | |
| (10:30-11:00) Break | ||
| Session 2: (11:00-12:30) Oral Presentations: Cancer Genetics and Pathway Curation | ||
| 11:00 | GRO Task: Populating the Gene Regulation Ontology with events and relations Jung-Jae Kim, Xu Han, Vivian Lee and Dietrich Rebholz-Schuhmann | |
| 11:10 | Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013 Sampo Pyysalo, Tomoko Ohta and Sophia Ananiadou | |
| 11:20 | Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013 Tomoko Ohta, Sampo Pyysalo, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Sophia Ananiadou and Jun’ichi Tsujii | |
| 11:30–11:50 | Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics Haibin Liu, Karin Verspoor, Donald C. Comeau, Andrew MacKinlay and W John Wilbur | |
| 11:50–12:10 | Performance and limitations of the linguistically motivated Cocoa/Peaberry system in a broad biological domain SV Ramanan and P. Senthil Nathan | |
| 12:10–12:30 | NaCTeM EventMine for BioNLP 2013 CG and PC tasks Makoto Miwa and Sophia Ananiadou | |
| (12:30-14:00) Lunch Break | ||
| Session 3: (14:00-15:30) Posters | ||
| BioNLP Shared Task 2013: Supporting Resources Pontus Stenetorp, Wiktoria Golik, Thierry Hamon, Donald C. Comeau, Rezarta Islamaj Dogan, Haibin Liu and W John Wilbur | ||
| A fast rule-based approach for biomedical event extraction Quoc-Chinh Bui, David Campos, Erik van Mulligen and Jan Kors | ||
| Improving Feature-Based Biomedical Event Extraction System by Integrating Argument Information Lishuang Li, Yiwen Wang and Degen Huang | ||
| UZH in BioNLP 2013 Fabio Rinaldi, Gerold Schneider, Simon Clematide, Tilia Ellendorff, Gintare Grigonyte and Don Tuggener | ||
| A Hybrid approach for biomedical event extraction Xuan Quang Pham, Minh Quang Le and Bao Quoc Ho | ||
| Identification of Genia Events using Multiple Classifiers Roland Roller and Mark Stevenson | ||
| Exploring a Probabilistic Earley Parser for Event Composition in Biomedical Texts Mai-Vu Tran, Nigel Collier, Hoang-Quynh Le, Van-Thuy Phi and Thanh-Binh Pham | ||
| Detecting Relations in the Gene Regulation Network Thomas Provoost and Marie-Francine Moens | ||
| Ontology-based semantic annotation: an automatic hybrid rule-based method Sondes Bannour, Laurent Audibert and Henry Soldano | ||
| Building A Contrasting Taxa Extractor for Relation Identification from Assertions: BIOlogical Taxonomy & Ontology Phrase Extraction System Cyril Grouin | ||
| Guest announcement: | ||
| The BioASQ project and challenges Ion Androutsopoulos | ||
| (15:30-16:00) Break | ||
| Session 4: (16:00-17:30) Oral Presentations: Bacteria: Gene Regulation Network and Biotope | ||
| 16:00 | BioNLP Shared Task 2013 – An overview of the Genic Regulation Network Task Robert Bossy, Philippe Bessières and Claire Nédellec | |
| 16:10 | BioNLP shared Task 2013 – An Overview of the Bacteria Biotope Task Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Philippe Bessières and Claire Nédellec | |
| 16:20–16:40 | Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules İlknur Karadeniz and Arzucan Özgür | |
| 16:40–17:00 | Extracting Gene Regulation Networks Using Linear-Chain Conditional Random Fields and Rules Slavko Zitnik, Marinka Žitnik, Bla Zupan and Marko Bajec | |
| 17:00–17:20 | IRISA participation to BioNLP-ST13: lazy-learning and information retrieval for information extraction tasks Vincent Claveau | |
| Session 5: (17:30-18:00) General Discussion |