Published online 13 November 2009 Nucleic Acids Research, 2010, Vol. 38, Database issue D415–D419 doi:10.1093/nar/gkp941 EuPathDB: a portal to eukaryotic pathogen databases Cristina Aurrecoechea 1 , John Brestelli2,3, Brian P. Brunk2,4, Steve Fischer2,3, Bindu Gajria2,4, Xin Gao2,4, Alan Gingle5, Greg Grant2,3, Omar S. Harb2,4,*, Mark Heiges1, Frank Innamorato2,3, John Iodice2,3, Jessica C. Kissinger1,6, Eileen T. Kraemer7, Wei Li2,4, John A. Miller7, Vishal Nayak2,3, Cary Pennington 1 , Deborah F. Pinney2,3, David S. Roos4, Chris Ross1, Ganesh Srinivasamoorthy1, Christian J. Stoeckert Jr2,3, Ryan Thibodeau 1 , Charles Treatman2,4 and Haiming Wang1 1Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, 2Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, 3Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, 5Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, 6Department of Genetics, University of Georgia, Athens, GA 30602 and 7Department of Computer Science, University of Georgia, Athens, GA 30602, USA Received September 16, 2009; Accepted October 10, 2009 ABSTRACT EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recently- implemented ‘search strategy’ system enables users to construct complex multi-step searches via a graphical interface. Search results are dynam- ically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users. INTRODUCTION The Eukaryotic Pathogen Database (EuPathDB) has been developed as a Bioinformatics Resource Center (BRC), with support from the US National Institutes of Health (NIH). Additional funding for a kinetoplastid component (TriTrypDB) was recently provided by the Bill and Melinda Gates Foundation, in coordination with indepen- dent support for kinetoplastid annotation from the Wellcome Trust. EuPathDB has undergone a dramatic expansion over the past two years, evolving from an apicomplexan-speciﬁc database (ApiDB) (1) to encompass additional non-apicomplexan pathogens of human and veterinary importance, most of which are classiﬁed as category B biodefense pathogens by the National Institute of Allergies and Infectious Diseases (NIAID). The eukaryotic pathogens included in EuPathDB are a major source of morbidity and mortality worldwide, causing millions of deaths and an immense economic burden. The current version of EuPathDB (version 2.1) serves as a portal for GiardiaDB (2), CryptoDB (3), PlasmoDB (4), ToxoDB (5), TrichDB (2) and TriTrypDB (companion paper in this issue). These databases provide access to genomic and functional genomic data for 22 species *To whom correspondence should be addressed. Tel: +1 215 746 7019; Fax: +1 215 573 3111; Email: oharb@pcbi.upenn.edu Correspondence may also be addressed to Brian P. Brunk. Tel: +1 215 573 3118; Fax: +1 215 573 3111; Email: brunkb@pcbi.upenn.edu Correspondence may also be addressed to Jessica C. Kissinger. Tel: +1 706 542 6562; Fax: +1 706 542 3582; Email: jkissing@uga.edu Correspondence may also be addressed to David S. Roos. Tel: +1 215 898 2118; Fax: +1 215 746 6697; Email: droos@sas.upenn.edu Correspondence may also be addressed to Christian J. Stoeckert. Tel: +1 215 573 4409; Fax: +1 215 573 3111; Email: stoeckrt@pcbi.upenn.edu The Author(s) 2009. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.