BioNLP 2023

SIGBIOMED

BIONLP 2016

An ACL 2016 Workshop associated with the SIGBIOMED special interest group Featuring two associated tasks: BioASQ ( http://www.bioasq.org/workshop) and BioNLP-ST (http://2016.bionlp-st.org).

Berlin, Germany, August 12 -13, 2016

TENTATIVE DATES

• Submission deadline: April - May, 2016
• Notification of acceptance: June, 2016
• Camera-ready copy due from authors: June, 2016
• Workshop: August 12, 2016
• Shared Tasks: August 13, 2016

WORKSHOP OVERVIEW AND SCOPE

Over the course of the past fourteen years, the ACL BioNLP workshop associated with the SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. The workshop serves as both a venue for bringing together researchers in bio- and clinical NLP and exposing these researchers to the mainstream ACL research, and a venue for informing the mainstream ACL researchers about the fast growing and important domain.

The workshop will continue presenting work on a broad and interesting range of topics in NLP.

The active areas of research include:

• Entity identification and normalization for a broad range of semantic categories
• Extraction of complex relations and events
• Semantic parsing
• Discourse analysis
• Anaphora /Coreference resolution
• Text mining
  • Literature based discovery
• Summarization
• Question Answering
• Resources and novel strategies for system testing and evaluation
  • Infrastructures for biomedical text mining
• Processing and annotation platforms
• Translating NLP research to practice
• Theoretical underpinnings of biomedical language processing

Tentative Program Committee:

• Emilia Apostolova, DePaul University, Chicago, USA
• Eiji Aramaki, University of Tokyo, Japan
• Sabine Bergler, Concordia University, Canada
• Olivier Bodenreider, National Library of Medicine, USA
• Aaron Cohen, Oregon Health and Science University, USA
• Nigel Collier, University of Cambridge, UK
• Noémie Elhadad, Columbia University, USA
• Marcelo Fiszman, National Library of Medicine, USA
• Filip Ginter, University of Turku, Finland
• Cyril Grouin, LIMSI - CNRS, France
• Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
• Halil Kilicoglu, National Library of Medicine
• Jin-Dong Kim, Database Center for Life Science, Japan
• Robert Leaman, National Library of Medicine, USA
• Zhiyong Lu, National Library of Medicine, USA
• Timothy Miller, Children's Hospital Boston, USA
• Makoto Miwa, Toyota Technological Institute, Japan
• Aurelie Neveol, LIMSI - CNRS, France
• Naoaki Okazaki, Tohoku University, Japan
• Jong Park, KAIST, Republic of Korea
• Sampo Pyysalo, University of Cambridge, UK
• Bastien Rance, Hopital Europeen Georges Pompidou
• Thomas Rindflesch, National Library of Medicine
• Kirk Roberts, National Library of Medicine
• Andrey Rzhetsky, University of Chicago
• Yoshimasa Tsuruoka, University of Tokyo, Japan
• Karin Verspoor, The University of Melbourne, Australia
• John Wilbur, National Library of Medicine
• Pierre Zweigenbaum, LIMSI - CNRS, France

Organizers

 * Kevin Bretonnel Cohen, University of Colorado School of Medicine
 * Dina Demner-Fushman, US National Library of Medicine
 * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK
 * Jun-ichi Tsujii, National Institute of Advanced Industrial Science and Technology, Japan 

Two tasks will be associated with the workshop this year:

The BioNLP Shared Task (BioNLP-ST) has been organized three times so far, leading to the development of information extraction systems for molecular biology and medicine in 2009, 2011 and 2013. One of the major contributions of BioNLP-ST is the availability of resources such as high quality manually curated corpora, tools, and evaluation services.

Shared Task Organizers:

• Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan
• Claire Nedellec, INRA, France
• Robert Bossy, INRA, France

The second equally successful shared task, the BioASQ challenge on large-scale biomedical semantic indexing and question answering has been running on an annual basis since 2012. The results of the challenge were presented in a workshop, which has so far been taking place in conjunction with the CLEF conference and was extremely well-attended.

BioASQ assesses the performance of information systems in supporting two tasks that are central in the biomedical question answering process: (a) the indexing of large volumes of unlabeled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generation of answers and supporting material. BioASQ has been making publicly available the following benchmark data and tools: more than 1300 questions and related answers, as well as online "oracle" for objective evaluation of any system throughout the year, not only during the challenge.

BioASQ Organizers:

• Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA
• Ioannis Kakadiaris University of Houston, USA
• Anastasia Krithara, NCSR "Demokritos", Greece