BioNLP Workshop

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An ACL 2016 Workshop associated with the SIGBIOMED special interest group Featuring two associated tasks: BioASQ ( and BioNLP-ST (

Berlin, Germany, August 12 -13, 2016


  • BioNLP workshop: Friday, August 12, 2016
  • BioNLP-ST and BioASQ workshop: Saturday August 13, 2016


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

We invite two types of submissions: full papers and short papers. Submissions are due by 11:59 PM EST on Sunday May 8, 2016.

Full papers should not exceed eight (8) pages of text, plus unlimited references. These are intended to be reports of original research. BioNLP aims to be the forum for interesting, innovative, and promising work involving biomedicine and language technology, whether or not yielding high performance at the moment. This by no means precludes our interest in and preference for mature results, strong performance, and thorough evaluation. Both types of research and combinations thereof are encouraged.

Short papers may consist of up to four (4) pages of content, plus unlimited references. Appropriate short paper topics include preliminary results, application notes, descriptions of work in progress, etc.

Electronic Submission

Submissions must be electronic and in PDF format, using the Softconf START conference management system at We strongly recommend the use of ACL LaTeX style files tailored for this year's conference. Submissions must conform to the official style guidelines. Style files and other information about paper formatting requirements will be made available on the conference website,

Submissions should be anonymous. Dual submission policy: papers may NOT be submitted to the BioNLP 2016 workshop if they are or will be concurrently submitted to another meeting or publication.

Tentative Program Committee:
  • Emilia Apostolova, DePaul University, Chicago, USA
  • Eiji Aramaki, University of Tokyo, Japan
  • Asma Ben Abacha, National Library of Medicine, USA
  • 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
  • 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, USA
  • Jin-Dong Kim, Database Center for Life Science, Japan
  • Robert Leaman, National Library of Medicine, USA
  • Ulf Leser, Humboldt-Universität zu Berlin, Germany
  • Zhiyong Lu, National Library of Medicine, USA
  • Timothy Miller, Children's Hospital Boston, USA
  • Makoto Miwa, Toyota Technological Institute, Japan
  • Danielle Mowery, University of Utah, USA
  • Yassine M'Rabet, National Library of Medicine, USA
  • Aurelie Neveol, LIMSI - CNRS, France
  • Nhung Nguyen, University of Manchester, UK
  • Naoaki Okazaki, Tohoku University, Japan
  • Jong Park, KAIST, Republic of Korea
  • Sampo Pyysalo, University of Cambridge, UK
  • Bastien Rance, Hopital Europeen Georges Pompidou, France
  • Fabio Rinaldi, University of Zurich, Switzerland
  • Thomas Rindflesch, National Library of Medicine
  • Angus Roberts, University of Sheffield, UK
  • Kirk Roberts, National Library of Medicine, USA
  • Yoshimasa Tsuruoka, University of Tokyo, Japan
  • Karin Verspoor, The University of Melbourne, Australia
  • Byron Wallace, University of Texas at Austin, USA
  • John Wilbur, National Library of Medicine, USA
  • Pierre Zweigenbaum, LIMSI - CNRS, France
 * 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