Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria

Jeremy D. Glasner 2 3 Guy Plunkett III 1 2 Bradley D. Anderson 2 3 David J. Baumler 2 3 Bryan S. Biehl 2 3 Valerie Burland 1 2 3 Eric L. Cabot 2 3 Aaron E. Darling 0 2 Bob Mau 2 3 Eric C. Neeno-Eckwall 2 3 David Pot 2 5 Yu Qiu 2 4 Anna I. Rissman 2 3 Sara Worzella 2 3 Sam Zaremba 2 5 Joel Fedorko 2 5 Tom Hampton 2 5 Paul Liss 2 3 Michael Rusch 2 3 Matthew Shaker 2 5 Lorie Shaull 2 5 Panna Shetty 2 5 Silpa Thotakura 2 5 Jon Whitmore 2 5 Frederick R. Blattner 1 2 3 John M. Greene 2 5 Nicole T. Perna 1 2 3 0 University of Queensland, Institute for Molecular Bioscience , St Lucia Q 4072, Australia 1 Laboratory of Genetics, University of Wisconsin , 425G Henry Mall, Madison, WI 53706, USA 2 livestock. The Enteropathogen Resource Integration Center (ERIC, www.ericbrc.org) is one of the eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases (http:// www.brc-central.org/). Funded by the National Institute of Allergy and Infectious Diseases (NIAID) , ERIC serves as an information resource for enterobacteria on the NIAID established list of select agents related to biodefense diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. ERIC seeks to support basic research on pathogenesis and development of novel vaccines , therapeutics and diagnostics for these organisms by: 3 Genome Center, University of Wisconsin , 425G Henry Mall, Madison, Madison, WI 53703 4 University of California , San Diego , Bioengineering , 9500 Gilman Drive, La Jolla, CA 92093, USA 5 SRA International , Inc., 11300 Rockville Pike, Suite 501, Rockville MD 20852 ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefensediarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats. - The family Enterobacteriaceae includes a variety of pathogens that pose significant threats to human health directly, and indirectly through agricultural crops and THE ERICBRC PORTAL OFFERS INTEGRATED ACCESS TO ALL TOOLS AND ANALYSES The ERICBRC is a web portal that provides a single point of access to information about the focus organisms. The web portal, implemented with the JBoss Application Server 4.05GA and JBoss Portal Server 2.4.1, provides a single, standardized method of accessing the diverse resources integrated into the system. In addition to the specific resources described in the sections below, the portal provides general information about pathogenic enterobacteria, summaries of the genome database contents, and links to other relevant databases, such as the Immune Epitope Database (1) a curated set of epitopes for the Category AC select agents. New functionalities and data sets are added to existing sections of the portal when appropriate or incorporated into new portlets within the main ERIC portal. This architecture permits rapid deployment of new components and customizable display of contents. ERICASAP GENOME ANNOTATIONS ERIC provides access to continuously updated genome annotations for all ERIC pathogens, as well as information from a variety of other enterobacteria useful for reference and comparison, including E. coli K-12 (Table 1). ERIC uses the ASAP genome annotation database system (2) using an Oracle 10 g database for genome annotation and curation. ERICASAP permits database updates continuously, obviating the need for periodic database releases that are a common feature of many genome databases. There are three general types of user accounts available for genome annotation purposes. Administrator accounts permit users the full range of capabilities including the ability to create new genome projects in the system. Curator accounts give users the ability to update ERIC annotations using sophisticated web-based interfaces for manual annotation and curation of information as well as tools for uploads of large sets of annotation data. Annotator accounts provide users with interfaces for manual annotation of individual annotation records. The annotation interfaces are all webbased and can be accessed by any member of the research community that requests an account. The availability of three different types of user accounts is designed to meet the needs of different types of annotators and to encourage training in use of the annotation tools that can be used to update large numbers of annotation records at a time. Genomes in ERIC can be either public or private projects, with users assigned to any of the three types of user accounts. All public genome sequence data and annotations, including any newly added information, are accessible without an account. Our goal is to provide genome annotations that are accurate, detailed, up-to-date and consistent across genomes. Descriptions of the standard operating procedures (SOPs) used by the ERIC curators are available for download from the portal (http://www.ericbrc.org/portal/ eric/aboutasap). Every annotation record includes a description of the evidence supporting the data, and this is the primary way we assess the quality of the annotation information and measure improvements over time. Explanations of the evidence codes and how they are used can be found in the SOP describing gene annotation (http://www.ericbrc.org/portal/eric/sopCdsAnnotation). ERICASAP is open for contribution by the research community to encourage annotation by domain experts. An additional layer of quality control is provided by a curation status tag for each annotation that indicates whether the information has been independently approved by one of a select group of trusted users and dedicated curators. Sequences and annotations in ERIC can be downloaded in a variety of formats including GenBank flatfile format and GFF3. Files downloaded directly from ERIC reflect continuous updates by the dedicated curatorial staff as well as community-contributed annotations. Snapshots of sequences annotated de novo by ERIC are also deposited in GenBank. Examples include the genome of Y. pestis strain CA88-4125 (GenBank accession number ABCD00000000) and plasmid pMAR7 from enteropathogenic Escherichia coli (3). ERIC is working (...truncated)