This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (6) Citing Articles via Google Scholar Google Scholar Articles by Bajic, V. B. Articles by Swarup, S. Search for Related Content PubMed PubMed Citation Articles by Bajic, V. B. Articles by Swarup, S. Agricola Articles by Bajic, V. B. Articles by Swarup, S.

BIOINFORMATICS

Dragon Plant Biology Explorer. A Text-Mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists^[w]

Knowledge Extraction Lab, Institute for Infocomm Research, Singapore 119613 (V.B.B., M.V., K.R., H.P.); and Department of Biological Sciences, National University of Singapore, Singapore 117543 (P.S.V., A.M., M.-W.H., S.S.)

We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with "omics" platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.060863.

^* Corresponding author; e-mail dbsss{at}nus.edu.sg; fax (65)–6779–2486.

Received February 7, 2005; returned for revision May 17, 2005; accepted May 23, 2005.

This article has been cited by other articles:

				M. Krallinger, C. Rodriguez-Penagos, A. Tendulkar, and A. Valencia PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction Nucleic Acids Res., July 1, 2009; 37(suppl_2): W160 - W165. [Abstract] [Full Text] [PDF]

				M. Kaur, A. Radovanovic, M. Essack, U. Schaefer, M. Maqungo, T. Kibler, S. Schmeier, A. Christoffels, K. Narasimhan, M. Choolani, et al. Database for exploration of functional context of genes implicated in ovarian cancer Nucleic Acids Res., January 1, 2009; 37(suppl_1): D820 - D823. [Abstract] [Full Text] [PDF]