BioNLP-ST Workshop

Date of the workshop: 9 August 2013
Location: Sofia, Bulgaria
Hosted by the ACL BioNLP workshop Workshop, 8-9 August 2013 in the ACL 2013 Conference
See the Schedule page for the deadlines
See Program below, with links to the papers on the ACL Anthology
Proceedings: Entire volume, Front Matter

Pre-submission phase

The submission Web site is open at for a "pre-submission phase" intended to collect descriptions of the participant teams and systems, which will be used to prepare the assignment of papers to reviewers, and which will help the task organizers include in their papers a synthesis of the results and participant methods. The questions include minimal information about your team, methods, and resources used in the challenge.

Deadline for pre-submission: April 26
Please submit title, authors, and description of participant team, methods, and resources. 

Submission phase

Paper submission proper will open at the same address on April 27.
Authors will still be able to revise their descriptions of teams and systems in that phase.

Participant papers can be submitted in two formats:
  • long paper, 8 pages plus up to 2 pages of references
  • short paper, 4 pages plus up to 2 pages of references
Submissions must be electronic and in PDF format, and should follow the two-column format of ACL proceedings. Please see the conference website for details. Authors are strongly encouraged to use the style files and formatting instructions available on the conference website: (scroll down)

Note however that contrary to the ACL main conference, authors' names should not be blinded, but rather included openly. In the context of the shared task, genuine anonymity would not be possible since published results will identify teams anyway.

Deadline for submission of papers: extended to May 3, 23:59 GMT-12 (closed)

Program: 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, Blaž 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
Pi Z,
Jun 18, 2013, 3:12 AM