PathwayFinder: paving the way towards automatic pathway extraction

Authors:
Daming Yao;Jingbo Wang;Yanmei Lu;Nathan Noble;Huandong Sun;Xiaoyan Zhu;Nan Lin;Donald G. Payan;Ming Li;Kunbin Qu
Affiliations:
University of Waterloo, Waterloo, Ontario, Canada;University of California at Santa Barbara, Santa Barbara, California, CA;Genentech Inc, San Francisco, CA;University of California at Santa Barbara, Santa Barbara, California, CA;University of California at Santa Barbara, Santa Barbara, California, CA;University of California at Santa Barbara, Santa Barbara, California, CA;Rigel Pharmaceuticals Inc, South San Francisco, CA;Rigel Pharmaceuticals Inc, South San Francisco, CA;University of California at Santa Barbara, Santa Barbara, California, CA;Rigel Pharmaceuticals Inc, South San Francisco, CA
Venue:
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Year:
2004

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Abstract

Automatically mining protein pathway information from the vast amount of published literature has been an increasing need from the pharmaceutical industry and biomedical research community. This task has been proved to be a formidable one. Many systems have been implemented, but few are practical. Some are too restricted and some are overly ambitious. 1This paper presents the PathwayFinder system with two key innovations that give the system simultaneously generalization power and practical capabilities: (a) PathwayFinder is designed with appropriate level of users' involvement on information extraction, based on the author's belief that totally automatic pathway retrieval is beyond the current technology; (b) A novel multi-agent architecture is built to support the need of user-computer interactions and domain extensions. As a result, PathwayFinder is flexible, easy to use, and extendable to be customized to other domains. We have successfully applied the PathwayFinder system to study the ubiquitin cascade pathway.