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ALICE: An Algorithm to Extract Abbreviations from MEDLINE

ALICE: An Algorithm to Extract Abbreviations from MEDLINE AbstractObjective: To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE (Abbreviation LIfter using Corpus-based Extraction). ALICE aims to extract all types of abbreviations with their expansions from a target paper on the fly.Methods: ALICE extracts an abbreviation and its expansion from the literature by using heuristic pattern-matching rules. This system consists of three phases and potentially identifies valid 320 abbreviation-expansion patterns as combinations of the rules.Results: It achieved 95% recall and 97% precision on randomly selected titles and abstracts from the MEDLINE database.Conclusion: ALICE extracted abbreviations and their expansions from the literature efficiently. The subtly compiled heuristics enabled it to extract abbreviations with high recall without significantly reducing precision. ALICE does not only facilitate recognition of an undefined abbreviation in a paper by constructing an abbreviation database or dictionary, but also makes biomedical literature retrieval more accurate. This system is freely available at http://uvdb3.hgc.jp/ALICE/ALICE_index.html. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of the American Medical Informatics Association Oxford University Press

ALICE: An Algorithm to Extract Abbreviations from MEDLINE

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Publisher
Oxford University Press
Copyright
American Medical Informatics Association
ISSN
1067-5027
eISSN
1527-974X
DOI
10.1197/jamia.M1757
pmid
15905486
Publisher site
See Article on Publisher Site

Abstract

AbstractObjective: To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE (Abbreviation LIfter using Corpus-based Extraction). ALICE aims to extract all types of abbreviations with their expansions from a target paper on the fly.Methods: ALICE extracts an abbreviation and its expansion from the literature by using heuristic pattern-matching rules. This system consists of three phases and potentially identifies valid 320 abbreviation-expansion patterns as combinations of the rules.Results: It achieved 95% recall and 97% precision on randomly selected titles and abstracts from the MEDLINE database.Conclusion: ALICE extracted abbreviations and their expansions from the literature efficiently. The subtly compiled heuristics enabled it to extract abbreviations with high recall without significantly reducing precision. ALICE does not only facilitate recognition of an undefined abbreviation in a paper by constructing an abbreviation database or dictionary, but also makes biomedical literature retrieval more accurate. This system is freely available at http://uvdb3.hgc.jp/ALICE/ALICE_index.html.

Journal

Journal of the American Medical Informatics AssociationOxford University Press

Published: Sep 1, 2005

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