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Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

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 - Influenza Other Respir Viruses (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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Related in: MedlinePlus

Surveillance data search interface – (A) Influenza Research Database (IRD) data are accessed through a variety of different customized search interfaces in which commonly used search criteria are initially displayed. In the case of animal surveillance data, these include sampling location, host, and whether influenza virus was detected and sequenced. Branching logic is used to add additional search criteria based on other selections; choosing the “Select family by list” radio button pops up a new box with avian family names listed. (B) In addition to the commonly used criteria, IRD also allows for searching by other characteristics (e.g., host age, collection date, latitude and longitude coordinates of collection site) as advanced options.
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fig05: Surveillance data search interface – (A) Influenza Research Database (IRD) data are accessed through a variety of different customized search interfaces in which commonly used search criteria are initially displayed. In the case of animal surveillance data, these include sampling location, host, and whether influenza virus was detected and sequenced. Branching logic is used to add additional search criteria based on other selections; choosing the “Select family by list” radio button pops up a new box with avian family names listed. (B) In addition to the commonly used criteria, IRD also allows for searching by other characteristics (e.g., host age, collection date, latitude and longitude coordinates of collection site) as advanced options.

Mentions: One of the more significant, distinguishing aspects of the IRD in comparison with other influenza resources is the availability of avian and non-human mammalian surveillance data. Surveillance data can be searched by various host and surveillance sample characteristics (Figure 5) with the results returned in the form of a surveillance record list or a custom summary table that enables users to compare up to four characteristics in a two-dimensional table. Characteristics that can be compared include host taxonomy, age and health status, sample influenza test results, isolation location and date, and virus subtype. The IRD surveillance records include precise geospatial location in the form of latitude and longitude coordinates, which allows visualization of the surveillance locations on a Google Map (Figure 6). Spatial coordinates also allow surveillance records to be mapped relative to other geospatial entities, such as bird migratory flyways.


Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

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 - Influenza Other Respir Viruses (2012)

Surveillance data search interface – (A) Influenza Research Database (IRD) data are accessed through a variety of different customized search interfaces in which commonly used search criteria are initially displayed. In the case of animal surveillance data, these include sampling location, host, and whether influenza virus was detected and sequenced. Branching logic is used to add additional search criteria based on other selections; choosing the “Select family by list” radio button pops up a new box with avian family names listed. (B) In addition to the commonly used criteria, IRD also allows for searching by other characteristics (e.g., host age, collection date, latitude and longitude coordinates of collection site) as advanced options.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3345175&req=5

fig05: Surveillance data search interface – (A) Influenza Research Database (IRD) data are accessed through a variety of different customized search interfaces in which commonly used search criteria are initially displayed. In the case of animal surveillance data, these include sampling location, host, and whether influenza virus was detected and sequenced. Branching logic is used to add additional search criteria based on other selections; choosing the “Select family by list” radio button pops up a new box with avian family names listed. (B) In addition to the commonly used criteria, IRD also allows for searching by other characteristics (e.g., host age, collection date, latitude and longitude coordinates of collection site) as advanced options.
Mentions: One of the more significant, distinguishing aspects of the IRD in comparison with other influenza resources is the availability of avian and non-human mammalian surveillance data. Surveillance data can be searched by various host and surveillance sample characteristics (Figure 5) with the results returned in the form of a surveillance record list or a custom summary table that enables users to compare up to four characteristics in a two-dimensional table. Characteristics that can be compared include host taxonomy, age and health status, sample influenza test results, isolation location and date, and virus subtype. The IRD surveillance records include precise geospatial location in the form of latitude and longitude coordinates, which allows visualization of the surveillance locations on a Google Map (Figure 6). Spatial coordinates also allow surveillance records to be mapped relative to other geospatial entities, such as bird migratory flyways.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Show MeSH
Related in: MedlinePlus