PATRIC: The VBI PathoSystems Resource Integration Center

Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, M.; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, J.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, S. M.; Khudyakov, Y.; Meng, X. J.; Rupprecht, C.; Vinje, J.; Crasta, O. R.; Czar, M. J.; Dickerman, A.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, J. C.; Sobral, B. W. S.

The conceptual organization of the website is described in Figure 1 . The website's home page contains news, Figure 1 . Conceptual map of PATRIC website. Arrows show the relationship between the principal datatype on a page and related data on neighboring pages. Solid arrows represent 'drilling down' to more specific information (e.g. from genome to gene). Dashed arrows represent links between different views of conceptually similar data (e.g. between ortholog group and phylogenetic tree). This figure represents only a subset of the pages and links on the actual website. a navigation bar and the list of PATRIC organisms. Users can select their organism of interest from the list to access the corresponding organism category page. This page contains a table of genomes currently in our database with links to the three principal representations of individual genomes: the genome summary, genome browser and gene table. These pages allow users to view a summary of genome sequencing information and to identify specific genes and link to their corresponding gene, protein and pathway information pages. The gene information page displays the output of sequence analysis software run by the annotation pipeline, as well as curated data. Similarly, the protein information page displays InterProScan and TIGRfam alignments and associated information such as GO terms and EC numbers. For bacterial genomes, the pathway information page illustrates the protein's position in the organism's metabolic network and links to a wealth of information provided by PathwayTools.