PathBinderH Taxonomy-Sensitive Literature Access Using the Biological Taxonomy to Access.pdf

PathBinderH: Taxonomy-Sensitive Literature Access Bioinformatics, 21(10) (May 2005), pp. 2560-2562. Using the Biological Taxonomy to Access Biological Literature with PathBinderH J. Ding1,2, K. Viswanathan2,3,4, D. Berleant1,2,5,*, L. Hughes,1,2 E. S. Wurtele2,5,6, D. Ashlock2,5,7,?, J. A. Dickerson1,2,5, A. Fulmer8, and P. S. Schnable2,4,6,9 1Department of Electrical and Computer Engineering; 2Iowa State University, Ames, Iowa 50011, USA; 3Department of Industrial Engineering; 4Center for Plant Genomics; 5Virtual Reality Applications Center, and Lawrence Baker Center for Bioinformatics and Biological Statistics; 6Department of Genetics, Development, Cell Biology; 7Department of Mathematics; 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: berleant@ ?Currently at the Department of Mathematics and Statistics, University of Guelph, Ontario, Canada N1G 2W1 PathBinderH: Taxonomy-Sensitive Literature Access 2 Using the Biological Taxonomy to Access Biological Literature with PathBinderH 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: /PathBinderH. Source code and databases on request. Contact: berleant@ Supplementary information: A tutorial is at the tool Web site. A longer paper is at /berleant/s/paperPathBinderHreport.pdf. INTRODUCTION Automated text mining in biology has grown dramatically in recent years, fueled by its potential to support efforts to understand