Skip Navigation



Bioinformatics Advance Access published online on July 21, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti586
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/18/3658    most recent
bti586v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Gaudan, S.
Right arrow Articles by Rebholz-Schuhmann, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gaudan, S.
Right arrow Articles by Rebholz-Schuhmann, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 1, 2005
Revised June 20, 2005
Accepted July 14, 2005

Article

Resolving abbreviations to their senses in Medline

S. Gaudan 1*, H. Kirsch 1, and D. Rebholz-Schuhmann 1

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

* To whom correspondence should be addressed.
S. Gaudan, E-mail: gaudan{at}ebi.ac.uk


  Abstract

Motivation: Biological literature contains many abbreviations with one particular sense in each document. However, most abbreviations do not have a unique sense across the literature. Furthermore, many documents do not contain the long-forms of the abbreviations. Resolving an abbreviation in a document consists of retrieving its sense in use. Abbreviation resolution improves accuracy of document retrieval engines and of information extraction systems.

Results: We combine an automatic analysis of Medline abstracts and linguistic methods to build a dictionary of abbreviation/sense pairs. The dictionary is used for the resolution of abbreviations occurring with their long-forms. Ambiguous global abbreviations are resolved using Support Vector Machines that have been trained on the context of each instance of the abbreviation/sense pairs, previously extracted for the dictionary setup. The system disambiguates abbreviations with a precision of 98.9% for a recall of 98.2% (98.5% accuracy). This performance is superior in comparison to previously reported research work.

Availability: The abbreviation resolution module is available at http://www.ebi.ac.uk/Rebholz/software.html.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
D. Rebholz-Schuhmann, H. Kirsch, M. Arregui, S. Gaudan, M. Riethoven, and P. Stoehr
EBIMed--text crunching to gather facts for proteins from Medline
Bioinformatics, January 15, 2007; 23(2): e237 - e244.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
N. Okazaki and S. Ananiadou
Building an abbreviation dictionary using a term recognition approach
Bioinformatics, December 15, 2006; 22(24): 3089 - 3095.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. Zhou, V. I. Torvik, and N. R. Smalheiser
ADAM: another database of abbreviations in MEDLINE
Bioinformatics, November 15, 2006; 22(22): 2813 - 2818.
[Abstract] [Full Text] [PDF]

Home page
 J. Am. Med. Inform. Assoc.Home page
H. Liu, Z.-Z. Hu, M. Torii, C. Wu, and C. Friedman
Quantitative Assessment of Dictionary-based Protein Named Entity Tagging
J. Am. Med. Inform. Assoc., September 1, 2006; 13(5): 497 - 507.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.