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Bioinformatics Advance Access published online on March 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti381
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 29, 2004
Revised February 20, 2005
Accepted March 7, 2005

Applications note

Using the biological taxonomy to access biological literature with PathBinderH

J. Ding 1, K. Viswanathan 2, D. Berleant 3*, L. Hughes 1, E. S. Wurtele 4, D. Ashlock 5, J. A. Dickerson 3, A. Fulmer 6, and P. S. Schnable 7

1 Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, USA; Iowa State University, Ames, Iowa 50011, USA
2 Iowa State University, Ames, Iowa 50011, USA; Department of Industrial Engineering, Iowa State University, Ames, Iowa 50011, USA; Center for Plant Genomics, Iowa State University, Ames, Iowa 50011, USA
3 Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, USA; Iowa State University, Ames, Iowa 50011, USA; Virtual Reality Applications Center, and Lawrence Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA
4 Iowa State University, Ames, Iowa 50011, USA; Virtual Reality Applications Center, and Lawrence Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA; Department of Genetics, Development, & Cell Biology, Iowa State University, Ames, Iowa 50011, USA
5 Iowa State University, Ames, Iowa 50011, USA; Virtual Reality Applications Center, and Lawrence Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA; Department of Mathematics, Iowa State University, Ames, Iowa 50011, USA
6 Miami Valley Laboratories, The Procter & Gamble Co., 11810 E. Miami River Rd., Ross, Ohio 45061, USA
7 Iowa State University, Ames, Iowa 50011, USA; Center for Plant Genomics, Iowa State University, Ames, Iowa 50011, USA; Department of Genetics, Development, & Cell Biology, Iowa State University, Ames, Iowa 50011, USA; Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA

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


  Abstract

Summary: PathBinderH allows users to make queries that retrieve sentences and their containing abstracts from PubMed. The most significant aspect of PathBinderH is that users can specify biological taxa in order to limit searches to abstracts mentioning either the specified taxa, or their subordinate taxa, in the biological taxonomy. Although current project needs only require this function for plant taxa, the principle is extensible to the entire taxonomy.

Availability: www.plantgenomics.iastate.edu/PathBinderH. Source code and databases on request.

Supplementary information: A tutorial is at the tool Web site. A longer paper is at class.ee.iastate.edu/berleant/s/paperPathBinderHreport.pdf.


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