Text analytics for life science using the Unstructured Information Management Architecture

IBM Systems Journal,  Sept, 2004  by R. Mack,  S. Mukherjea,  A. Soffer,  N. Uramoto,  E. Brown,  A. Coden,  J. Cooper,  A. Inokuchi,  B. Iyer,  Y. Mass,  H. Matsuzawa,  L.V. Subramaniam

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Acknowledgments

BioTeKS is in large part a systems integration effort that builds on technologies and expertise developed by many groups in IBM Research. All these groups generously provided their time and expertise to deliver code to the BioTeKS team, teach us how to use it, and in some cases modify their code for our needs. These groups include the UIMA/JEDII team in Hawthorne (David Ferrucci, Adam Lally, and Jerry Cwiklik), the TALENT text analysis team (Roy Byrd, Mary Neff, Rie Ando, Bran Boguraev, and Youngja Park), the machine learning team (David Johnson, Sylvie Levesque, Tong Zhang, Frank Oles, and Brian White), and research management at various levels for support and technical direction (Alan Marwick, Marshall Schor, Arthur Ciceolo, Ajay Royyuru, and Kohichi Takeda). Additional colleagues at other IBM Research locations were involved in various applications cited in this paper. These colleagues include Ravi Kothar, Pankaj Kankar, Biplav Srivastava, Vishal Batra, Krishna Kummamuru, and Pasumarti Kamesam at India Research; Jeff Kreulen, Dan Gruhl, and Shivakumar Vaithaynathan at Almaden Research; and Tetsuya Nasukawa at Tokyo Research. We also thank Tony Eng (MIT graduate student) for useful comments on early drafts of this paper, and four other anonymous reviewers whose careful reading greatly improved this paper. Colleagues in business units also provided opportunities for learning about real-world customer requirements. These include Michael Hehenberger, Avijit Chatterjee, Usha Reddy, Edwin Hilpert, Stephen Boyer, John Christina, Peter Libal, Thilo Gotz, Thomas Hampp, Deb Sutherland, Lance Snow, Eric Will, Jeff Tenner, Dave Herbeck, Erik Voldal, Bryan Tousley, Joanna Batstone, Beth Smith, and of course, Carol Kovac.

* Trademark or registered trademark of International Business Machines Corporation.

** Trademark or registered trademark of United States National Library of Medicine, Institut Suisse de Bioinformatique (SIB) Foundation, Intel Corporation, or Linus Torvalds.

Cited references and notes

(1.) Pharma2010: The Threshold of innovation, IBM Corporation (2002), http://www-1.ibm.com/industries/healthcare/doe/ content/resource/thought/390030105.html.

(2.) W.C. Swope, "Deep Computing for the Life Sciences," IBM Systems Journal 40, No. 2, 284-262 (2001), http://www. research.ibm.com/journal/sj/402/swope.html.

(3.) J. Augen, "The Evolving Role of Information Technology in the Drug Discovery Process," Drug Discovery Today 7, No. 5, 315-323 (March 2002).

(4.) D. Ferrucci and A. Lally, "Building an Example Application with the Unstructured Information Management Architecture," IBM Systems Journal 43, No. 3, 455-475 (2004, this issue).

(5.) D. Ferrucci and A. Lally, "Accelerating Corporate Research in the Development, Application and Deployment of Human Language Technologies," Proceedings of the Workshop on Software Engineering and Architecture of Language Technology Systems (SEALTS), Edmonton, CA (May 31, 2003).