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Nucleic Acids Research 2006 34(Web Server issue):W748-W752; doi:10.1093/nar/gkl194
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

botXminer: mining biomedical literature with a new web-based application

Uma Mudunuri, Robert Stephens, David Bruining, David Liu and Frank J. Lebeda1,*

Science Applications International Corporation-Frederick, Advanced Biomedical Computing Center, SAIC-Frederick Inc., National Cancer Institute-Frederick Frederick, MD 21702, USA 1 US Army Medical Research Institute for Infectious Diseases, Integrated Toxicology Division Fort Detrick, MD 21702-5011, USA

*To whom correspondence should be addressed: Tel: +1 301 619 4279; Fax: +1 301 619 2348; Email: frank.lebeda{at}amedd.army.mil

Received February 21, 2006. Revised March 21, 2006. Accepted March 21, 2006.

This paper outlines botXminer, a publicly available application to search XML-formatted MEDLINE® data in a complete, object-relational schema implemented in Oracle® XML DB. An advantage offered by botXminer is that it can generate quantitative results with certain queries that are not feasible through the Entrez-PubMed® interface. After retrieving citations associated with user-supplied search terms, MEDLINE fields (title, abstract, journal, MeSH® and chemical) and terms (MeSH qualifiers and descriptors, keywords, author, gene symbol and chemical), these citations are grouped and displayed as tabulated or graphic results. This work represents an extension of previous research for integrating these citations with relational systems. botXminer has a user-friendly, intuitive interface that can be freely accessed at http://botdb.abcc.ncifcrf.gov.


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R. Z. Cer, U. Mudunuri, R. Stephens, and F. J. Lebeda
IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W441 - W445.
[Abstract] [Full Text] [PDF]


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