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

Abstract

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/.

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

“…In addition, text-mining results based on similar procedure as used in (21,22) and a few manually curated datasets for TFs of particular interest (see Supplementary Section 1 for details) were also utilized as sources.…”

PMRD: a curated database for genes and mutants involved in plant male reproduction

“…In such papers, information is often organized into discernable sections, such as initial characterization of a gene, gene expression assays, and morphological phenotype observations, etc. Two text-mining tools are currently available for the Arabidopsis [42,43]; it is hoped that such text-processing software will be used in future updates and maintenance of the database.…”

Hierarchical Biological Pathway Data Integration and Mining

“…There has been a dramatic increase in the number of large scale comprehensive biological databases that provide useful resources to the community like; Biochemical Pathways (KEGG, AraCyc, and MapMan), Protein Interactions (biomolecular interaction network database), or systems like; Dragon Plant Biology Explorer and Pathway Miner for integrating associations in metabolic networks and ontologies [3][4][5][6][7][8]. Other databases such as Regulon DB, PlantCARE, PLACE, EDP:Eurokaryotic promoter database, Transcription Regulatory Regions Database, Athamap, and TRANSFAC store information related to transcriptional regulation [9][10][11][12][13][14][15].…”