TY - JOUR
T1 - BioHealthBase
T2 - Informatics support in the elucidation of influenza virus host-pathogen interactions and virulence
AU - Squires, Burke
AU - Macken, Catherine
AU - Garcia-Sastre, Adolfo
AU - Godbole, Shubhada
AU - Noronha, Jyothi
AU - Hunt, Victoria
AU - Chang, Roger
AU - Larsen, Christopher N.
AU - Klem, Ed
AU - Biersack, Kevin
AU - Scheuermann, Richard H.
N1 - Funding Information:
influenza virus physiology and pathogenesis. While several public database resources provide focused data sets about influenza virus isolates (e.g. sequence records), the BioHealthBase emphasizes the integration of data from public resources together with data derived from various analysis and prediction algorithms, allowing researchers to explore hypotheses using bio-informatics approaches before heading into the laboratory. The BioHealthBase places significant emphasis on supporting data related to host–pathogen interactions in order to gain a better understanding of the nature of virulence and host range, and the impact of sequence variation on these phenomena. Current plans for future enhancements of the BioHealthBase BRC resource include the ability to construct phylogenetic trees based on sequence relationships, the definition of functional sequence features in influenza proteins and their availability for display in both the genome browser and the 3D protein structure visualization module, and the support for surveillance and research data produced by the Centers of Excellence for Influenza Research and Surveillance program recently funded by NIAID (http://www3.niaid.nih.gov/research/resources/ ceirs/).
Funding Information:
We thank the Reactome database project team, especially Marc Gillespie, Peter D’Eustachio and Lincoln Stein for their assistance with the development and deployment of the influenza life cycle representation. We also thank Aihui Wang, Bjoern Peters, Gillian Air, Feng Luo and Valentina Di Francesco for advice on various components of the BioHealthBase. The BioHealthBase Bioinformatics Resource Center has been wholly funded with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. N01-AI40041. Funding to pay the Open Access publication charges for this article was provided by NIH Contract No. N01-AI40041.
PY - 2008/1
Y1 - 2008/1
N2 - The BioHealthBase Bioinformatics Resource Center (BRC) (www.biohealthbase.org) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens - Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin. The BioHealthBase serves as an extensive integrated repository of data imported from public databases, data derived from various computational algorithms and information curated from the scientific literature. The goal of the BioHealthBase is to facilitate the development of therapeutics, diagnostics and vaccines by integrating all available data in the context of host-pathogen interactions, thus allowing researchers to understand the root causes of virulence and pathogenicity. Genome and protein annotations can be viewed either as formatted text or graphically through a genome browser. 3D visualization capabilities allow researchers to view proteins with key structural and functional features highlighted. Influenza virus host-pathogen interactions at the molecular/cellular and systemic levels are represented. Host immune response to influenza infection is conveyed through the display of experimentally determined antibody and T-cell epitopes curated from the scientific literature or as derived from computational predictions. At the molecular/cellular level, the BioHealthBase BRC has developed biological pathway representations relevant to influenza virus host-pathogen interaction in collaboration with the Reactome database (www.reactome.org).
AB - The BioHealthBase Bioinformatics Resource Center (BRC) (www.biohealthbase.org) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens - Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin. The BioHealthBase serves as an extensive integrated repository of data imported from public databases, data derived from various computational algorithms and information curated from the scientific literature. The goal of the BioHealthBase is to facilitate the development of therapeutics, diagnostics and vaccines by integrating all available data in the context of host-pathogen interactions, thus allowing researchers to understand the root causes of virulence and pathogenicity. Genome and protein annotations can be viewed either as formatted text or graphically through a genome browser. 3D visualization capabilities allow researchers to view proteins with key structural and functional features highlighted. Influenza virus host-pathogen interactions at the molecular/cellular and systemic levels are represented. Host immune response to influenza infection is conveyed through the display of experimentally determined antibody and T-cell epitopes curated from the scientific literature or as derived from computational predictions. At the molecular/cellular level, the BioHealthBase BRC has developed biological pathway representations relevant to influenza virus host-pathogen interaction in collaboration with the Reactome database (www.reactome.org).
UR - http://www.scopus.com/inward/record.url?scp=38549147460&partnerID=8YFLogxK
U2 - 10.1093/nar/gkm905
DO - 10.1093/nar/gkm905
M3 - Article
C2 - 17965094
AN - SCOPUS:38549147460
SN - 0305-1048
VL - 36
SP - D497-D503
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -