An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data

Zhang, C.; Crasta, O.; Cammer, S.; Will, R.; Kenyon, R.; Sullivan, D.; Yu, Q.; Sun, W.; Jha, R.; Liu, D.; Xue, T.; Zhang, Y.; Moore, M.; McGarvey, P.; Huang, H.; Chen, Y.; Zhang, J.; Mazumder, R.; Wu, C.; Sobral, B.

To facilitate community research for discovery of candidates for the next generation of vaccines, therapeutics and diagnostics, the National Institute of Allergy and Infectious Diseases (NIAID) has funded research to characterize pathogen proteomes and pathogen:host interactions, and mechanisms of pathogenesis, which includes contracts to seven PRCs that generate diverse experiment data sets from multiple pathosystems, and a Biodefense Proteomics Resource Center (RC) to store the data, provide visualization and analysis tools, and make it publicly accessible (for a complete list of organisms under investigation see the RC home page http://www.proteomicsresource.org/). Towards this goal, the RC is hosted across three institutions (SSS, VBI, PIR) and includes a variety of information and tools covering the organisms, reagents, publications, operating procedures, protein annotations, experiment data and more. These are highly linked to maximize the value to the research community. The remainder of this article will focus on one aspect of the RC, the public proteomics repository system which was developed with the following main objectives: (i) manage and disseminate transcriptomic and proteomic data; (ii) develop a cyberinfrastructure (http://www.nsf. gov/od/oci/reports/toc.jsp) for integration and interoperability of diverse data sets. The RC is a unique publicly available proteomics data resource that hosts a wide range of 'omics' data sets on pathogen and host interactions and integrates all experiment data submitted by PRCs to illustrate gene or protein functions involved in pathogen biology, and host and pathogen interaction.