Bioinformatics Vol. 19 no. 13 2003
Pages 1699-1706
© 2003 Oxford University Press
MedScan, a natural language processing engine for MEDLINE abstracts
Ariadne Genomics, Inc., 9100 Great Seneca HWY, Rockville, MD 20850, USA
Received on January 11, 2003
; revised on February 11, 2003
; accepted on March 17, 2003
Motivation: The importance of extracting biomedical information from scientific publications is well recognized. A number of information extraction systems for the biomedical domain have been reported, but none of them have become widely used in practical applications. Most proposals to date make rather simplistic assumptions about the syntactic aspect of natural language. There is an urgent need for a system that has broad coverage and performs well in real-text applications.
Results: We present a general biomedical domain-oriented NLP engine called MedScan that efficiently processes sentences from MEDLINE abstracts and produces a set of regularized logical structures representing the meaning of each sentence. The engine utilizes a specially developed context-free grammar and lexicon. Preliminary evaluation of the system's performance, accuracy, and coverage exhibited encouraging results. Further approaches for increasing the coverage and reducing parsing ambiguity of the engine, as well as its application for information extraction are discussed.
Availability: MedScan is available for commercial licensing from Ariadne Genomics, Inc.
Contact: nikolai{at}ariadnegenomics.com
* To whom correspondence should be addressed.
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