EuPathDB: the eukaryotic pathogen genomics database resource

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

A unique infrastructure and search strategy system distinguish the Eukaryotic Pathogen Database Resource (EuPathDB, http://eupathdb.org) from other organism databases. The power of EuPathDB lies in the ability to query across hundreds of data sets while refining a set of genes, proteins, pathways or organisms of interest. The interface is designed for easy mastery by biological researchers, enabling in silico experiments that interrogate diverse and complex data sets. Despite the sophisticated strategy system, browsing gene pages and genomic spans or regions remains a simple and informative task in this innovative and valuable resource. EuPathDB facilitates the discovery of meaningful biological relationships between genomic features such as genes or SNPs by integrating pre-analyzed data with sophisticated data mining, visualization and analysis tools that are designed to be used by wet-bench researchers. Organized into 13 free, online databases EuPathDB supports over 170 eukaryotic pathogens with genomic sequence and annotation, functional genomics data, host-response data, isolate and population data and comparative genomics. Table 1 provides a web address and a link to a list of organisms supported for each database. All databases are built with the same infrastructure and use the Strategies Web Development Kit (1) , which provides a graphical interface for building complex search strategies and exploring relationships across data sets and data types ( Figure 1 ; strategy http://plasmodb.org/plasmo/im.do?s=7b88206dd42007c8).