An Emerging Cyberinfrastructure for Biodefense Pathogen and Pathogen-host Data

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2007 Nov 7

PMID 17984082

Citations 5

Authors

C Zhang

O Crasta

S Cammer

R Will

R Kenyon

D Sullivan

Q Yu

W Sun

R Jha

D Liu

T Xue

Y Zhang

M Moore

P McGarvey

H Huang

Y Chen

J Zhang

R Mazumder

C Wu

B Sobral

Affiliations

Soon will be listed here.

Abstract

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/.

Citing Articles

PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.

Gillespie J, Wattam A, Cammer S, Gabbard J, Shukla M, Dalay O Infect Immun. 2011; 79(11):4286-98.

PMID: 21896772 PMC: 3257917. DOI: 10.1128/IAI.00207-11.

HPIDB--a unified resource for host-pathogen interactions.

Kumar R, Nanduri B BMC Bioinformatics. 2010; 11 Suppl 6:S16.

PMID: 20946599 PMC: 3026363. DOI: 10.1186/1471-2105-11-S6-S16.

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data.

Chen C, McGarvey P, Huang H, Wu C Adv Bioinformatics. 2010; :423589.

PMID: 20369061 PMC: 2847380. DOI: 10.1155/2010/423589.

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

McGarvey P, Huang H, Mazumder R, Zhang J, Chen Y, Zhang C PLoS One. 2009; 4(9):e7162.

PMID: 19779614 PMC: 2745575. DOI: 10.1371/journal.pone.0007162.

A mapping of drug space from the viewpoint of small molecule metabolism.

Adams J, Keiser M, Basuino L, Chambers H, Lee D, Wiest O PLoS Comput Biol. 2009; 5(8):e1000474.

PMID: 19701464 PMC: 2727484. DOI: 10.1371/journal.pcbi.1000474.

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