Mining the Biomedical Literature

Acknowledgments

As Selim Akl kindly pointed out at the very early stages of this endeavor, writing a book can be a pretty lonely job. However, as it turned out, our interaction with students and colleagues throughout this time— conversations, discussions, debates, and arguments, both public and private—all helped to shape and sharpen the ideas presented in this book. We would like to thank the many people who have contributed to our understanding and to our view of all that is discussed in this book, as well as those whose friendship and support made it possible for us to actually write it. Many thanks go to our colleagues and collaborators in the biomedical text mining excursion,especially:Lynette Hirschman,Christian Blaschke, Alfonso Valencia, Russ Altman, Sophia Ananiadou, Lan Aronson, Christopher Baker, Sabine Bergler,Ted Briscoe, Bob Carpenter, Monica Chagoyen, Kevin Cohen, Aaron Cohen, Marc Colosimo, Dina DemnerFushman , Anna Divoli, Ian Donaldson, Dave Eichmann, Noemie Elhadad, Carol Friedman, Udo Hahn, Marti Hearst, Bill Hersh, Eivind Hovig, Larry Hunter, Lars Jensen, Su Jian, Nikiforos Karamanis, Ian Lewin, Marc Light, Anália Lourenço, David McClosky, Yves Moreau, Alex Morgan, Sean O’donoghue, Alberto Pascual-Montago, Hoifung Poon, Sampo Pyysalo, Dietrich Rebholz-Schuhmann, Phoebe Roberts, Luis Rocha, Patrick Ruch,Andrey Rzhetsky, Padmini Srinivasan, Jun’ichi Tsujii, Karin Verspoor, Anne-Lise Veuthey, Anita de Waard, Mark Weeber, Bonnie Webber, Cathy Wu, Alex Yeh, Hong Yu, Ralf Zimmer, and the many others who have been part of the vivid discussions at TREC Genomics, BioCreative, BioLINK, and BioNLP workshops. From all the above, we are particularly thankful to Lan Aronson for the information he provided about MeSH indexing, to Sean O’donoghue for the image of the Reflect system, to Eivind Hovig for the image of PubGene, as well as to Kevin Cohen who was a firm-enough believer Acknowledgments x Acknowledgments in the book so as to start referencing it quite a few years before its completion. Special thanks are due to JohnWilbur for introducing HS to biomedical text in the first place and to Mark Boguski and Stephen Edwards for being her first biological partners venturing into this area. Colleagues and collaborators from several fields, with whom our interactions have always been stimulating and have often given rise to new research directions, are: Paul Ahlquist, Vineet Bafna, Asa Ben-Hur, Dorothea Blostein, Chris Bradfield, William Cohen, Art Delcher, John Denu, Dan Fasulo, Mike Flanigan, Iddo Friedberg, Lew Friedland, Ronen Feldman, Michael Gould, Annette Höglund, Jeanette Holden, Nathalie Japkowicz, Oliver Kohlbacher, Johan Kumlien, Stan Matwin, Jason Miller, Clark Mobarry, Parvin Mousavi, Robert Murphy, Sharon Regan, Hershel Safer, Ron Stewart,EllenVoorhees,ShibuYooseph,MalikYousef,and Jerry Zhu.We thank all of them, and do apologize for unintentional omission of any names. Both of us were fortunate enough to have several people who acted as mentors throughout the years, providing knowledge, insight, guidance and advice on science and on writing, along with encouragement and opportunities to pursue the directions leading to this book. For HS, these include Catriel Be’eri, Leslie Pack Kaelbling, Tom Dean, Gene Myers, Sorin Istrail and Granger Sutton. For MC, they include Jude Shavlik,Tom Mitchell and Dave DeMets. We are sincerely grateful to all of them. HS also thanks both her former department chairs at Queen’s University , Jim Cordy and Selim Akl, for supporting her in taking on the book writing, as well as Errol Lloyd, her department chair at the University of Delaware, for his consideration, which allowed her to complete it. Many of our excellent students and postdocs explored some of the fundamental ideas presented in this book and helped demonstrate their value. Others helped us in exploring and learning about related ideas. HS thanks Scott Brady, Fengxia Pan, Rob Denroche, Phil Hyoun Lee, Andrew Wong, Jess Shen, Nawei Chen,Yin Lam, Quazi Abidur Rahman, Zhi Hong Zheng, Na Harrington, Limin Zheng, and Sara Salehi. MC thanks Dave Andrzejewski, Joe Bockhorst, Debbie Chasman, Deborah Muganda, Keith Noto, Irene Ong, Yue Pan, Soumya Ray, Burr Settles, Marios Skounakis, Adam Smith, and Andreas Vlachos. We are grateful to our editors at MIT Press—Bob Prior, for keeping his high spirits and belief in this project over several long years, Susan Buckley and Katherine Almeida for shepherding the book through the xi Acknowledgments production process—and to Sorin Istrail, the series editor, who invited us to write the book with MIT Press in the first place. In terms of the biological...