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Nucleic Acids Research Advance Access published online on November 4, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm903
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data

C. Zhang1, O. Crasta1, S. Cammer1, R. Will1, R. Kenyon1, D. Sullivan1, Q. Yu1, W. Sun1, R. Jha1, D. Liu1, T. Xue1, Y. Zhang1, M. Moore2, P. McGarvey3, H. Huang3, Y. Chen2,3, J. Zhang2,3, R. Mazumder3, C. Wu3 and B. Sobral1,*

1Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University, Washington Street (0477), Blacksburg, VA 24061, 2Social & Scientific Systems, Inc., 8757 Georgia Avenue, 12th Floor Silver Spring, MD 20910 and 3Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC 20007, USA

*To whom correspondence should be addressed. Tel: +1 540 231 2100; Fax: +1 540 231 2606; Email: sobral{at}vbi.vt.edu

Received August 15, 2007. Revised October 4, 2007. Accepted October 5, 2007.

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host–pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.


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