D418 Nucleic Acids Research, 2010, Vol. 38, Database issue Unlike queries available through the organism-speciﬁc component databases, where users are restricted to datasets available in that particular database, the EuPathDB user has the opportunity to explore data from all organisms represented on any component site. This expanded range provides the ability to transform a set of results from one organism into its orthologs in another, making it possible to generate comparable lists of results in organisms where particular functional data are lacking. Execution of queries in EuPathDB starts by selecting a type of search from the options shown in Figure 1D. A strategy expands upon the ﬁrst search (Step 1) by adding additional searches using set operators such as union, intersect and minus (graphically displayed with Venn diagrams, Figure 1E). Any step in the strategy can be transformed into orthologs from selected species of interest. Figure 1E presents an example in which orthology is leveraged between organisms to generate a list of potential apicoplast (plastid-like organelle) targeted genes in Toxoplasma using information from other species. In step one, genes predicted to target to the parasite-speciﬁc apicoplast arganelle in P. falciparum are obtained based on available targeting information data (7). This list is transformed into orthologs in the related species T. gondii in step two, yielding 138 candidates. In step three, this list is restricted by subtract- ing genes found in Cryptosporidium (a related organism that has lost its apicoplast), leaving 86 possible Toxoplasma apicoplast-targeted genes. Many of these genes have been experimentally proven to target to the apicoplast, validating this approach. Analogous search strategies can be used to generate a wide variety of poten- tially useful gene lists, such as: genes in Toxoplasma and Giardia that are orthologs of oocyst genes in Cryptosporidium and Plasmodium (for which functional data are available); or orthologous genes expressed in the Plasmodium and Trypanosoma arthropod stages; or genes for which reagents are available (such as antibodies) in other organisms. Steps in a strategy can be renamed, revised, viewed, deleted, downloaded or expanded into sub-strategies. In addition, whole strategies can be renamed, saved, copied, closed/opened, deleted or shared with others via a uniquely generated URL (a recipient of the URL can click on it to generate the strategy in their own workspace). Previously executed strategies can be accessed via ‘Browse Strategies’ by clicking on the appro- priate tab (Figure 1E). Results are dynamically updated below the strategy in an interactive summary table (Figure 1F, green box) that allows a user to click on the number of genes under the component database to ﬁlter the results revealing only genes from that database or all databases by clicking on the ‘all results’ link. The actual gene list appears dynam- ically below the summary table (Figure 1G) and can be sorted, expanded with additional columns of data (Figure 1H) or downloaded. Detailed gene information can be viewed by visiting speciﬁc gene pages, which are accessed by clicking on the gene IDs in the result list (Red box in Figure 1I). In an eﬀort to promote community involvement in annotation, users can enter comments on gene and isolate record pages. Such comments can include PubMed IDs (references are automatically retrieved for ﬁnal display in the comment), GenBank accession numbers, ﬁles (such as images), and comments that apply to multiple gene or isolate records can be easily replicated by adding the related IDs to the comment form. Comments immediately appear on record pages and become indexed and searchable via the text search. This feature has positively contributed to genome curation eﬀorts in general and has speciﬁcally improved the oﬃcial annotation of the P. falciparum and Trypanosomatidae genomes (see companion TriTrypDB paper for further information). Users of EuPathDB and its family of databases can also upload ﬁles to a community ﬁle repos- itory that provides a venue for users to share data that are not linked to a speciﬁc record, such as, protocols. FUTURE DIRECTIONS The EuPathDB family of databases is expected to expand further over the coming years, incorporating new species including the Amoebozoa (Entamoeba, Acanthamoeba), Microsporidia, and additional Apicomplexans, Kinetoplastida and Diplomonads. Features and tools will continue to be introduced and improved, such as the ability to make connections between diverse data types, a basket for users to place cherry-picked genes for subsequent manipulation and weighting of queries to enable more eﬀective analysis of complex strategy results. Of course, we also anticipate that data will continue to be deposited at an ever-increasing rate, including additional genome sequences, microarray data, probe-based hybridization and sequencing data (e.g. ChIP-chip and RNA-Seq), proteomics data, isolate data, phenotype information, metabolomic data, etc. ACKNOWLEDGEMENTS The authors wish to acknowledge the contribution of numerous members of the eukaryotic pathogen research community, in the form of advice, suggestions and/or data—often made available to the community via EuPathDB and its components in advance of publication. FUNDING EuPathDB is funded with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400037C (to D.S.R., C.J.S. and J.C.K.). The TriTrypDB component is supported by grant no. 50096 from the Bill and Melinda Gates Foundation. Funding for open access charge: National Institutes of Health. Conﬂict of interest statement. None declared.