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Bioinformatics Vol. 17 no. 90001 2001
Pages S74-S82
© 2001 Oxford University Press

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

Carol Friedman 1,2, Pauline Kra 2, Hong Yu 2, Michael Krauthammer 2 and Andrey Rzhetsky 2,3

1 Computer Science Dept, Queens College CUNY, Flushing, NY, 11367, USA
2 Department of Medical Informatics, Columbia University, New York, 10032, USA
3 Genome Center, Columbia University, New York, 10032, USA

Received on January 31, 2001 ; revised on March 30, 2001 ; accepted on March 30, 2001

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.

Contact: friedman.carol{at}dmi.columbia.edu


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