Using the biological taxonomy to access biological literature with PathBinderH

J Ding; K Viswanathan; D Berleant; L Hughes; E S Wurtele; D Ashlock; J A Dickerson; A Fulmer; P S Schnable

doi:10.1093/bioinformatics/bti381

Using the biological taxonomy to access biological literature with PathBinderH

Bioinformatics. 2005 May 15;21(10):2560-2. doi: 10.1093/bioinformatics/bti381. Epub 2005 Mar 15.

Authors

J Ding¹, K Viswanathan, D Berleant, L Hughes, E S Wurtele, D Ashlock, J A Dickerson, A Fulmer, P S Schnable

Affiliation

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

PMID: 15769838
DOI: 10.1093/bioinformatics/bti381

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Abstracting and Indexing / methods*
Biology / methods
Database Management Systems*
Documentation / methods*
Information Storage and Retrieval / methods
Natural Language Processing*
Periodicals as Topic*
Plants / classification*
PubMed*
Software*
Vocabulary, Controlled