Dragon plant biology explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists

We introduce a tool for textmining,DragonPlantBiologyExplorer (DPBE) that integrates information onArabidopsis (Arabidopsis thaliana) geneswith their functions, basedongeneontologies andbiochemical entity vocabularies, andpresents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by TheArabidopsis 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 onmetabolic pathways, enzymes, and metabolites derived fromAraCyc, BRENDA, and othermetabolismdatabases.Wedemonstrate howvarious combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry andmetabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with ‘‘omics’ ’ platformoutputs.Using a list of abiotic stress-relatedgenes identifiedbymicroarray experiments,we showhowthis 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 tomake better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers andgraduate students to summarize vast information in anunfamiliar area.DPBE is freely available for academic and nonprofit users a