Professional

Professional Activities

Professional Advisory or Consultancy Work

  • Advisory Board, Elsevier, SciVerse 2010-
  • BBSRC Pool of Experts (January 2010 –December 2011)
  • Agence Nationale de la Recherche, CONTINT (2010)
  • Swiss National Foundation (2010)
  • Consultant for ITI Life Sciences, Scotland, Biomedical Text Mining (2005)
  • External assessor for the CLAMOUR project, coordinated by the Office for National Statistics (2001)

Offices Held

  • Vice-president of the European Association for Terminology (EAFT) 1997-1999

Advisory or Review Work for Funding Bodies

  • Reviewer for EPSRC since 2001, BBSRC since 2005 and JISC since 2006
  • External reviewer to the National Medical Research Council, Singapore, 2009
  • External reviewer to the Global Centers of Excellence (COE) Program, Ministry of Education,Culture, Sports, Science and Technology (MEXT), Japan, 2009
  • Advisor to the National ICT Australia Victoria Research Laboratory, Department of Computer Science and Software Engineering, University of Melbourne (2007)
  • Advisor for the Israel Science Foundation (2005)
  • External advisor to the Netherlands Organisation for Scientific Research (2004)
  • External panel member for the Greek Ministry of Research and Technology for research proposals in Language Technology (1999).
  • Expert Advisory Group on Language Engineering Standards (EAGLES); a long-term initiative (running since 1991) sponsored by the European Commission. Subgroup Coordinator (1997-1999)
  • Invited by DTI as sole academic member of an OSTEMS fact-finding mission to visit leading IT companies in Japan, joining a group of 6 speech and natural language processing experts from British industry (1996).

Conference Chair

  • Co-chair, 2011, International Workshop on Data and Text Mining in Biomedical Informatics, in conjunction with 20th ACM Conference on Information and Knowledge Management
  • Session Chair, Computational Methods and Tools, 11th International Conference on Systems Biology (ICSB 2010)
  • Area Chair in Text Mining and Natural Language Processing Applications, ACL-IJCNLP, Singapore, 2009
  • Area Chair in Biomedical Text Mining : Genomes to Systems conference, 2008, Manchester
  • Area Chair for demos/posters ACL 2007, Prague
  • Chair Semantic Mining in Biomedicine (SMBM) Conference, 2006, Jena

Workshop Organiser or Co-Organiser

  • Coling 2016, Osaka, Japan, Building and Evaluating Resources for Biomedical Text Mining with R. Bastista-Navarro, K. Cohen, D. Demner-Fushman and P. Thompson
  • ACL, BioNLP, 2016, Berlin, Germany with D. Demner-Fushman, US National Library of Medicine; K. Cohen, U. Colorado School of Medicine; J. Tsujii, National Institute of Advanced Industrial Science and Technology, Japan and University of Manchester, UK
  • ACL, BioNLP, 2015, Beijing, China with D. Demner-Fushman, US National Library of Medicine; K. Cohen, U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, National Institute of Advanced Industrial Science and Technology, Japan
  • ACL, BioNLP, 2014, Baltimore, MD with D. Demner-Fushman, US National Library of Medicine; K. Cohen, U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, Microsoft Research Asia, China
  • LREC 2014, Reykjavik, Iceland, Building and Evaluating Resources for Health and Biomedical Text Processing with K. Choukri, K. Cohen, D. Demner-Fushman, J. Hajic, A. Hanbury, G. Jones, H. Müller, P. Pecina and P. Thompson
  • ACL, BioNLP, 2013, Sofia, Bulgaria, with D. Demner-Fushman, Lister Hill National Center for Biomedical Communications; K. Cohen, U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, Microsoft Research Asia, China & U. Manchester
  • LREC 2012, Istanbul, Turkey, Building and Evaluating Resources for Biomedical Text Mining with D. Demner-Fushman, K. Cohen and P. Thompson
  • NAACL, BioNLP, 2012, Montreal, Canada, with D. Demner-Fushman, Lister Hill National Center for Biomedical Communications; K. Cohen, U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, U. Tokyo, Japan & U. Manchester, and B. Webber, U. of Edinburgh.
  • ACL, BioNLP, 2011, Oregon, Portland, with D. Demner-Fushman, Lister Hill National Center for Biomedical Communications; K. Cohen, U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, U. Tokyo, Japan & U. Manchester, and B. Webber, U. of Edinburgh.
  • ACL, BioNLP, 2010, Uppsala, Sweden, with D. Demner-Fushman, US National Library of Medicine; K. Cohen, U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, U. Tokyo, Japan & U. Manchester, and B. Webber, U. of Edinburgh.
  • LREC 2010, Malta, Building and Evaluating Resources for Biomedical Text Mining with D. Demner-Fushman and K. Cohen
  • NAACL-HLT, BioNLP, 2009, Colorado, with D. Demner-Fushman, US National Library of Medicine; K. Cohen, The MITRE Corporation; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, U. Tokyo, Japan & U. Manchester, and B. Webber, U. of Edinburgh.
  • ACL, BioNLP 2008, June 2008, Ohio with D. Demner-Fushman, US National Library of Medicine; K. Cohen, The MITRE Corporation and U. Colorado School of Medicine; J. Pestian, Computational Medicine Center, Cincinnati Children’s Hospital and Medical Center; J. Tsujii, U. Tokyo, Japan & U. Manchester, and B. Webber, U. of Edinburgh.
  • LREC 2008, Building and evaluating resources for biomedical text mining, May 2008 with M. Monachini, Istituto di Linguistica Computazionale, Italy; Goran Nenadic, University of Manchester, and Jian Su, Institute for Infocomm Research, Singapore.
  • ESRC, NCeSS, Agenda Setting Workshop, Bridging quantitative and qualitative methods using text mining in social sciences, 2006 and 2008, with R. Procter.
  • Medical Informatics Europe 2005, with O. Bodenreider, National Library of Medicine, USA, Terminologies and Ontologies, Geneva, Switzerland.
  • Coling 2004, with P. Zweigenbaum, (STIM/DSI/CRIM/INALCO), Computational Terminology, CompuTerm 2004, Geneva, Switzerland.
  • International Joint Conference of Natural Language Processing, Text Mining in Biomedicine, with J. Park, Korea Advanced Institute of Science and Technology, 2004, Hainan Island, China.
  • ACL 2003, Natural Language Processing techniques in Biomedicine, workshop associated with the Association for Computational Linguistics Conference, Sapporo, Japan with J. Tsujii.
  • Natural Language Processing, 2000, Computational Terminology for Medical and Biological Applications, Greece with D. Maynard.
  • Machine Translation Summit VII, Machine Translation for Cross-Language Information Retrieval (CLIR), Singapore, 1999.

Conference Programme Committee Member  (Selected)

  • International Conference on Computational Linguistics (COLING) 1996, 1998, 2000, 2002, 2004, 2010
  • Pacific Symposium on Biocomputing (PSB) 2000-2001, 2006-2007, 2008
  • International Conference on Intelligent Systems for Molecular Biology (ISMB) 2003-2010
  • European Conference on Computational Biology (ECCB) 2005, 2007-2008
  • Association for Computational Linguistics (ACL) 2000, 2007-2011
  • EMNLP/VLC (2000) Joint SIGDAT Conference on Empirical Methods in NLP and very large corpora, Hong Kong.
  • International Conference on Language Resources and Evaluation (LREC) 2000-2010
  • SMBM-2008, Third International Symposium on Semantic Mining in Biomedicine, 2008

Referee for Journals (Selected)

  • Bioinformatics
  • BMC Bioinformatics
  • International Journal of Terminology
  • Medical Informatics Journal
  • Briefings in Bioinformatics
  • PloS Computational Biology
  • PloS ONE
  • Computational Intelligence

Workshop Programme Committee Member (Selected)

  • Linking Literature, Information and Knowledge for Biology Special Interest Group on Text Mining (ISMB) 2007
  • IJCAI 2007 Workshop on Analytics for Noisy Unstructured Text Data
  • HLT/ NACCL 2006, BioNLP’06: Linking Natural Language Processing and Biology: Towards deeper biological literature analysis
  • Workshop on Biomedical Ontologies and Text Processing, ECCB’05
  • International Symposium on Semantic Mining in Biomedicine, EC Network of Excellence on Semantic Mining & EBI, 2005
  • Coling 2004 Workshop: International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
  • BioCreative 2004 & 2007
  • Linking Biological Literature, Ontologies and Databases: Tools for Users, Workshop in conjunction with NAACL/ HLT 2004, Boston, USA