(Second) Call for Papers Linking Natural Language Processing and Biology: Towards deeper biological literature analysis (BioNLP'06) bionlp_workshop_2006@lanl.gov An HLT-NAACL'06 workshop New York City June 8, 2006 http://compbio.uchsc.edu/BioNLP06 NOTE: DEADLINE HAS BEEN EXTENDED TO MARCH 01. This workshop will bring researchers in text processing in the bioinformatics and biomedical domains together to discuss how techniques from natural language processing and information retrieval can be exploited to address biological information needs. We invite papers on recent, substantial, original and unpublished research in this area. The workshop will be part of the HLT-NAACL 2006 meeting (http://nlp.cs.nyu.edu/hlt-naacl06/), hosted by New York University in New York City. The workshop is being sponsored by Procter & Gamble, and we thank P&G for their support. WORKSHOP SCOPE There remain significant challenges in biological literature exploitation, in particular for such biological problem areas as automated function prediction and pathway reconstruction and linguistic applications such as relation extraction and abstractive summarization. In the light of these remaining challenges, the focus of this workshop will be on applications that move towards deeper semantic analysis. We are particularly interested in work that addresses relatively under-explored areas such as summarization and question-answering from biological information. Papers describing applications of semantic processing technologies to the biology domain are especially invited. That is, the primary topics of interest are applications which require deeper linguistic analysis of the biological literature, or issues in porting NLP systems originally constructed for other domains to the biology domain. What makes the biology domain special? What hurdles must be overcome in performing linguistic analysis of biological text? Are any special linguistic or knowledge resources required beyond a domain-specific lexicon? What relations in biological text are most interesting to biologists, and hence should be the focus of our future efforts? However, submissions on all topics related to natural language processing in the bioinformatics, biomedicine, and molecular biology domains are welcome, including: - new application areas of NLP for addressing biological analysis problems - issues in the portability of NLP systems to the biology domain - relationship extraction from biological text - question answering for biology - summarization of biological information - coreference and anaphora resolution - lexical semantics for the biology domain - the role of ontologies and knowledge bases in understanding biomedical texts - knowledge representation - evaluation and testing of systems - test suites for biomedical language processing systems - entity identification and normalization - information extraction - information retrieval - automated categorization of biological texts - corpus construction efforts - visualization KEYNOTE ANDREY RZHETSKY has agreed to be the Keynote speaker at the workshop. Andrey is Associate Professor in the Department of Biomedical Informatics in the Judith P. Suzberger MD Columbia Genome Center of the Center for Computational Biology and Bioinformatics at Columbia University. His webpage can be found at http://genome6.cpmc.columbia.edu/andrey/. IMPORTANT DATES Paper submission due: March 01, 2006 (11:59pm EST) Notification of acceptance: March 31, 2006 Camera-ready paper due: April 16, 2006 Workshop: June 8, 2006 SUBMISSION GUIDELINES We invite two types of submissions: full papers and poster abstracts. Submissions are due by 11:59pm EST on March 01, 2006. Please submit your paper or abstract via the workshop submission site at http://www.softconf.com/start/HLT-WS06-BioNLP. Full papers should not exceed eight (8) pages including references. These are intended to be reports of original and mature research. Poster abstracts should not exceed two (2) pages. Accepted abstracts will be published in a separate section of the workshop proceedings. Appropriate poster topics include preliminary results, application notes, descriptions of work in progress, etc. Format: Submissions must be electronic and in PDF format, and should follow the two-column format of ACL proceedings. Please see the conference website for detailed typesetting specifications. Authors are strongly encouraged to use the LaTeX or Microsoft Word style files available on the website (http://nlp.cs.nyu.edu/hlt-naacl06/styles/index.html). Authors who cannot submit a PDF file electronically should contact the workshop organizers. Reviewing: The reviewing of submissions will be blind. Do not include author names in the paper. Avoid self-references -- instead of "As we showed in Seuss et al. 1999...", say "As Seuss et al. 1999 showed...." Please do include a list of authors in the email that accompanies the submission. Each submission will be reviewed by at least two program committee members. Submission procedure: Please submit your paper at http://www.softconf.com/start/HLT-WS06-BioNLP/ A PDF file of the paper must be submitted via the conference submission page, or if web-based submission is not possible to bionlp_workshop_2006@lanl.gov via email, by 11:59pm EST of the deadline. Papers submitted after that time will not be reviewed. Along with your submission, please indicate the title, complete author list, and email address of the corresponding author for the submission. Since reviewing will be blind, do not include the author names in the submission itself. ORGANIZING COMMITTEE bionlp_workshop_2006@lanl.gov Karin Verspoor Los Alamos National Laboratory Kevin Bretonnel Cohen U. Colorado, Center for Computational Pharmacology Ben Goertzel Biomind LLC Inderjeet Mani MITRE PROGRAM COMMITTEE Aaron Cohen Oregon Health & Science University Alexander Morgan MITRE Alfonso Valencia Centro Nacional de Biotecnologia, Universidad Autonoma, Madrid Andrey Rzhetsky Columbia University Ben Wellner MITRE Bob Carpenter Alias I, Inc. Bonnie Webber University of Edinburgh Breck Baldwin Alias I, Inc. Carol Friedman Columbia University Christian Blaschke Bioalma (Madrid) Hagit Shatkay Queen's University Henk Harkema University of Sheffield Hong Yu Columbia University Jeffrey Chang Duke Institute for Genome Sciences and Policy Jun-ichi Tsujii National Center for Text Mining, UK and University of Tokyo Lan Aronson National Library of Medicine Larry Hunter University of Colorado Health Sciences Center Lorraine Tanabe National Library of Medicine Luis Rocha University of Indiana Lynette Hirschman MITRE Marc Light University of Iowa Mark Mandel University of Pennsylvania Marti Hearst UC Berkeley Olivier Bodenreider National Library of Medicine Patrick Ruch University Hospital of Geneva and Swiss Federal Institute of Technology Robert Futrelle Northeastern University Sophia Ananiadou National Center for Text Mining, UK and University of Manchester Thomas Rindflesch National Library of Medicine Vasileios Hatzivassiloglou University of Texas at Dallas W. John Wilbur National Library of Medicine SPONSORS We would like to thank Procter & Gamble for their financial contribution in support of this workshop. Please direct any questions to bionlp_workshop_2006@lanl.gov. Workshop URL: http://compbio.uchsc.edu/BioNLP06