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ERIC News
  
Welcome to ERIC! - the Enteropathogen Resource Integration Center.

ERIC is one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.  

Yersinia SNP studies in ERIC
Lawrence Berkeley National Laboratories and Perlegen Sciences, Inc. recently completed a study of Single Nucleotide Polymorphisms (SNPs) in Yersinia, supported by a Cooperative Research for the Development of Vaccines, Adjuvants, Therapeutics, Immunotherapeutics, and Diagnostics for Biodefense and SARS grant from the National Institute of Allergy and Infectious Diseases (NIAID). A total of 2975 SNPs were validated across 147 strains of Yersinia pestis and pseudotuberculosis. You can read about the project and access the data here, with links to the appropriate pages in ASAP for the completed (i.e. non-draft) genomes in ERIC.

Virulence Genes in ERIC
ERIC introduces an easier way to research virulence genes. From the Genome Tools page, you can now select from a list of known and putative virulence factors to see and download relevant annotations, sequences, encoded portions, and other detailed information.

ERIC Introduces Literature Text Mining
Using a powerful, proven text mining technology from SRA, ERIC now processes PubMed abstracts daily to present the Latest Articles in the past week relevant to enteropathogens. Click on Text Mining under the Genomes Tools menu bar above to see the recent articles, or to search PubMed abstracts (beyond just enteropathogens) by keyword, PubMed ID, or within a date range. All results show the PubMed abstract highlighted with extracted entities (such as genes and mutations), their roles, and relationships with those entities.

Request an Account
Participate in the ERIC community. ERIC has a new portal page for obtaining a user account. Request a free account to annotate genomes. Your input is extremely valuable.

Training: Introduction to ERIC-BRC
Please join us for a web-enabled live demo of ERIC-BRC. This quick introduction to our bioinformatics portal will introduce you to the most commonly used features and workflows for finding, adding, and analyzing genomic and proteomic data associated with our enteropathogens. We welcome requests for ad hoc training sessions; visit the registration page for more detailed information.

Literature Text Mining
   
NetOwlThe most recent week's enteropathogen related abstracts from PubMed are available here, analyzed by ERIC-NetOwl to extract relevant facts on bacterial genomics. Click here for a full page listing.
Ignore Articles With No Relations Extracted
1. PMID 19007965: Photocatalytic inactivation of E. coli in surface water using immobilised nanoparticle TiO(2) films.
2. PMID 19008134: Enhancement of humoral and cellular immunity in mice against Japanese encephalitis virus using a DNA prime-protein boost vaccine strategy.
3. PMID 19007789: Ribosomal Intersubunit Bridge B2a Is Involved in Factor-Dependent Translation Initiation and Translational Processivity.
4. PMID 19006976: Swine health impact on carcass contamination and human foodborne risk.
5. PMID 19006978: Risk factors for infection with pathogenic and antimicrobial-resistant fecal bacteria in northern elephant seals in California.
Returned 119 Articles    Page: 
Data Summaries
   




Annotation Summary
 
Genes CDS rRNA tRNA misc_RNA pseudogenes EC # GO ID IS Elements Unique PubMed ID
Total 467,693 452,153 1,709 7,451 1,271 5,109 72,713 306,798 7,055 2,417
Changed 443,537 431,923 1,223 5,718 920 3,753 72,322 308,390 7,055 2,417


Genome Summary
 
Class of Organism Complete Draft Total
Escherichia 14 22 36
Salmonella 9 17 26
Shigella 8 2 10
Yersinia 9 14 23
Other Genomes 6 0 6
Totals: 46 55 101

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Annotations
Displays comprehensive annotations, history, sequence, external DB links, etc.
   Perlegen SNP Data    Virulence Genes in ERIC    Guide to Annotation    ERIC Annotation SOPs

BLAST
Displays results of protein or nucleotide BLAST for query sequence.

Graphical Genome Browser
Displays query location and content on respective genome(s).

Microarray Analysis:
An integrated set of web-based analysis tools and a data management system for storing and analyzing gene expression data.
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Mauve
Rapid alignment of multiple whole genomes.

Text Mining
Uses text mining technology to retrieve user-selected PubMed abstracts and to display functional relationships for genes and other biological molecules.

Latest Genome Additions
  

ERIC Genomes