Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

IRD

General information

URL: https://www.fludb.org/
Full name: Influenza Research Database
Description: A U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research.
Year founded: 2009
Last update: 2018-11-28
Version:
Accessibility:
Manual:
Accessible
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Country/Region: United States
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: J. Craig Venter Institute
Address: 4120 Capricorn Lane
City: La Jolla
Province/State: California
Country/Region: United States
Contact name (PI/Team): Richard H. Scheuermann
Contact email (PI/Helpdesk): rscheuermann@jcvi.org

Publications

27679478
Influenza Research Database: An integrated bioinformatics resource for influenza virus research. [PMID: 27679478]
Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH.

The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2017:45(D1) | 91 Citations (from Europe PMC, 2021-06-19)
22260278
Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. [PMID: 22260278]
Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, Ramsey A, Zhou L, Zaremba S, Kumar S, Deitrich J, Klem E, Scheuermann RH.

The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics. © 2012 Blackwell Publishing Ltd.

Influenza Other Respir Viruses. 2012:6(6) | 152 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
341/5061 (93.282%)
Health and medicine:
73/1067 (93.252%)
Structure:
30/700 (95.857%)
341
Total Rank
243
Citations
27
z-index

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Record metadata

Created on: 2017-02-16
Curated by:
[2018-11-28]
Lina Ma [2017-06-15]
Shixiang Sun [2017-02-16]