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Bioinformatics Advance Access originally published online on March 15, 2005
Bioinformatics 2005 21(10):2560-2562; 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{at}oupjournals.org

Using the biological taxonomy to access biological literature with PathBinderH

J. Ding 1,2, K. Viswanathan 2,3,4, D. Berleant 1,2,5,*, L. Hughes 1,2, E. S. Wurtele 2,5,6, D. Ashlock 2,5,7,{dagger}, J. A. Dickerson 1,2,5, A. Fulmer 8 and P. S. Schnable 2,4,6,9

1Department of Electrical and Computer Engineering, Iowa State University Ames, IA 50011, USA
2Iowa State University Ames, IA 50011, USA
3Department of Industrial Engineering, The Procter & Gamble Co. 11810 E. Miami River Rd., Ross, Ohio 45061, USA
4Center for Plant Genomics, The Procter & Gamble Co. 11810 E. Miami River Rd., Ross, Ohio 45061, USA
5Virtual Reality Applications Center, and Lawrence Baker Center for Bioinformatics and Biological Statistics, The Procter & Gamble Co. 11810 E. Miami River Rd., Ross, Ohio 45061, USA
6Department of Genetics, Development, and Cell Biology, The Procter & Gamble Co. 11810 E. Miami River Rd., Ross, Ohio 45061, USA
7Department of Mathematics, The Procter & Gamble Co. 11810 E. Miami River Rd., Ross, Ohio 45061, USA
8Miami Valley Laboratories, The Procter & Gamble Co. 11810 E. Miami River Rd., Ross, Ohio 45061, USA
9Department of Agronomy

*To whom correspondence should be addressed.

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

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

Contact: berleant{at}iastate.edu

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


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