EuPathDB: a portal to eukaryotic pathogen databases

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 dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.

Figure 1.

Screen shots from the EuPathDB database. (A) Interactive banner present on all EuPathDB web pages, including quick search windows and a tool bar (grey). (B) Side bar components contain expandable sections for release notes, community resources, tutorials and help (new items are highlighted with a yellow alert). (C) Hyperlinked logos of the EuPathDB component sites direct users to component databases. (D) Gene searches, non-gene entity searches, such as ESTs, ORFs of genome sequence and useful tools (BLAST against genomes in EuPathDB, PubMed records pertaining to EuPathDB organisms etc.). Note: clicking on the “+” symbol reveals a list of searches available within each category. (E) A multi-step search strategy, leveraging orthology to identify apicoplast targeted genes in Toxoplasma. (F) Summary table that allows filtering results based on component sites. (G) The results of a search strategy appear dynamically as the strategy is built and modified. (H) Additional columns of data can be added to results list. (I) Individual gene pages in the component sites can be accessed by clicking on their gene IDs.