Skip Navigation



Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti087
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/5/694    most recent
bti087v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 Ding, J.
Right arrow Articles by Berleant, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ding, J.
Right arrow Articles by Berleant, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received May 21, 2004
Revised September 13, 2004
Accepted October 7, 2004

Applications note

MedKit: A helper toolkit for automatic mining of MEDLINE/PubMed citations

Jing Ding 1 and Daniel Berleant 1*

1 Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA

* To whom correspondence should be addressed.
Daniel Berleant, E-mail: berleant{at}iastate.edu


  Abstract

Summary: MEDLINE/PubMed is one of the most important information sources for bioinformatics text mining. However, there remain limitations in working with MEDLINE/PubMed citations. For example, PubMed imposes an upper limit of 10,000 for downloading PMID list or citations; and MEDLINE files are too large for most off-the-shelf XML parsers. We developed a Java package, MedKit, to work-around the limitations, as well as provide other useful functionalities, e.g. random sampling. Its four modules (querier, sampler, fetcher and parser) can work independently, or be pipelined in various combinations. It can be used as a stand-alone GUI application, or integrated into other text mining systems. Text mining researchers and others may download and use the toolkit free for non-commercial purposes.

Availability: http://metnetdb.gdcb.iastate.edu/medkit.


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




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.