D416 Nucleic Acids Research, 2010, Vol. 38, Database issue Table 1. Species and data types included in the EuPathDB family of databases Genomic sequence EST SAGE tag Microarray Proteomic RNA-Seq SNP Isolate ChIP-chip/ ChIP-seq CryptoDB GiardiaDB PlasmoDB ToxoDB TrichDB TriTrypDB EuPathDB C. hominis C. parvum C. muris G. lamblia WB P. falciparum P. vivax P. yoelii P. knowlesi P. berghei P. chabaudi P. gallinaceum P. reichenowi T. gondii N. caninum T. vaginalis T. brucei T. cruzi L. major L. infantum L. braziliensis L. tarentolae Related species Data anticipated by March, 2010 is indicated in red. EuPathDB related species include genomic sequences for Theileria parva and annulata and EST sequences for Eimeria spp., Babesia spp., Sarcocystis spp., Theileria spp., Neospora hughesi and Gregarina niphandordes. (Table 1). In addition, EuPathDB provides access to genomic and/or expressed sequence tag data for additional related apicomplexan and trypanosomatid species (Table 1). Users can access functional data directly via the component web sites or through EuPathDB where query execution retrieves data from the component sites via Web services. One advantage of running searches in EuPathDB is the ability to leverage functional data from the diverse organisms we support and combine the search results based on orthology (6). The diversity of functional genomics data available through EuPathDB continues to expand dramatically (Table 1) making it essential to provide clients with an interface that is functional, user-friendly and sophisticated (Figure 1). To this end, we have recently introduced a novel search system enabling users to build complex queries comprised of indi- vidual searches (steps) that are linked with each other using set operations (union, intersection, and minus) (Figure 1D). WHAT IS NEW IN EuPathDB Over the past two years EuPathDB (formerly ApiDB) has evolved from an apicomplexan-speciﬁc resource (CryptoDB, PlasmoDB and ToxoDB) to encompass pro- tozoan pathogens outside this phylum, doubling its reper- toire of functional genomic databases (GiardiaDB and TrichDB in early 2008, and TriTrypDB in early 2009). Concurrent with this expansion, EuPathDB has under- gone dramatic changes speciﬁcally designed to enhance data accessibility and provide database users with a graphical query-building interface that eﬀectively creates a venue for constructing complex search strategies with relative ease. The EuPathDB homepage provides the user with quick and easy access to information by providing speciﬁc, func- tional sections (Figure 1A–D), a design feature that is replicated across EuPathDB component sites. The top part of the page (banner) remains constant throughout EuPathDB Web pages, providing quick access to text- and gene ID-based searches, links to useful pages (help and information pages, a ‘Contact Us’ link, registration/ login), and a tool bar (gray) with links to access diverse searches (see below), the user’s personal search history, tools, downloads, data sources, and other links (Figure 1A). The left side of the home page (Figure 1B) provides a series of expandable windows containing news items (release notes, etc.), tutorials (demonstrating the website), community resources, and additional informa- tion and help. The number of new items added since the user’s last visit is indicated by yellow numbers. The middle of the page includes hyperlinked logos for all EuPathDB component sites, providing direct access to taxon-speciﬁc databases (Figure 1C). Below, three sections provide access to queries and tools (Figure 1D): (i) gene-centric searches allowing the identiﬁcation of genes based on text terms, species, transcript and protein expression, GO terms, EC numbers, user deﬁned protein motif patterns, phylogenetic proﬁle, etc.; (ii) other data type searches such as isolates and their geographic or clinical origin, expressed sequence tags (ESTs), single nucleotide polymorphism (SNP) data, etc.; (iii) access to useful tools such as BLAST, the sequence retrieval tool, metabolic pathways and PubMed records.