ToxoDB: an integrated genomic database for the study of Toxoplasma gondii and Neospora caninum

Integrated databases resources are integral to the study of biology and of host-pathogen interactions. Tremendous strides in technology have permitted the generation of large, valuable data sets for many life cycle stages of numerous pathogens and/or their hosts. The Toxoplasma genome database (http://ToxoDB.org) currently hosts, and integrates, a wide array of diverse, large-scale data sets (1). ToxoDB contains three fully annotated genome sequences for Toxoplasma gondii (GT1, VEG and ME49 strains) and the annotated genome sequence of the closely related Neospora caninum (2). Additionally, the database contains all available EST sequence data, 13 microarray experimental datasets for tachyzoites and bradyzoites, 2 SAGETag data sets, 1 tachyzoite RNA-Seq experiment from both T. gondii VEG and N. caninum, and ChIP-on-chip data sets from precipitation with several different histone antibodies. The database also contains 21 proteomic data sets, SNPs and ortholog and synteny determinations between all Toxoplasma strains and Neospora. The database is part of the NIH-funded Eukaryotic Pathogen Database, (http://EuPathDB.org) (3). The integrated data are presented in an intuitive interface that permits strategic data mining across the data sets using our strategy system (4). For example, it is possible to identify all annotated genes that contain a signal peptide, are expressed in tachyzoites, but not bradyzoites, have evidence of protein expression and are conserved in Neospora with only a few clicks of the cursor. The database, which has been in existence since 2003 (5), is a free community resource that is linked to other prominent apicomplexan organisms (Plasmodium, Thileria, Babesia and Cryptosporidium) as well as other prominent eukaryotic pathogens (Giardia, Entamoeba, Leishmania, Trypanosoma, Microsporidia and Trichomonas) via the EuPathDB.org portal. The EuPathDB portal permits queries of Toxoplasma and any other organism contained within the database simultaneously. For example, it is possible to search for genes with certain properties that are conserved in Toxoplasma and Neospora but not other Apicomplexa. References 1. Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, et al. ToxoDB: An integrated Toxoplasma gondii database resource. Nucleic Acids Res. 2008;36(Database issue):D553-6.http://www.sanger. ac.uk/resources/downloads/protozoa/neosporacaninum.html. 2. Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, et al. EuPathDB: A portal to eukaryotic pathogen databases. Nucleic Acids Res. 2010;38(Database issue):D415-9. 3. Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, et al. The strategies WDK: A graphical search interface and web development kit for functional genomics databases. DATABASE The Journal of Biological Databases and Curation. In press. 4. Kissinger JC, Gajria B, Li L, Paulsen IT, Roos DS. ToxoDB: Accessing the Toxoplasma gondii genome. Nucleic Acids Res. 2003;31:234-6.